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<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by keeping only the last one.
"""
records = {acc: (rec, get_record_type(rec)) for acc, rec in
SeqIO.index(fastafn, 'fasta').items()}
proteins = ((x,) for x in records.keys())
sequences = ((acc, str(rec.seq)) for acc, (rec, rtype) in records.items())
desc = ((acc, get_description(rec, rtype)) for acc, (rec, rtype) in records.items() if rtype)
evid = ((acc, get_uniprot_evidence_level(rec, rtype)) for acc, (rec, rtype) in
records.items())
ensgs = [(get_ensg(rec), acc) for acc, (rec, rtype) in records.items()
if rtype == 'ensembl']
def sym_out():
symbols = ((get_symbol(rec, rtype, fastadelim, genefield), acc) for
acc, (rec, rtype) in records.items() if rtype)
othergene = ((get_other_gene(rec, fastadelim, genefield), acc) for acc, (rec, rtype) in records.items()
if not rtype and fastadelim and fastadelim in rec.description)
yield from symbols
yield from othergene
return proteins, sequences, desc, evid, ensgs, [x for x in sym_out()]
def parse_fasta(fn):
<|fim_middle|>
def get_record_type(record):
dmod = get_decoy_mod_string(record.id)
test_name = record.id
if dmod is not None:
test_name = record.id.replace(dmod, '')
if test_name.split('|')[0] in ['sp', 'tr']:
return 'swiss'
elif test_name[:3] == 'ENS':
return 'ensembl'
else:
return False
def get_decoy_mod_string(protein):
mods = ['tryp_reverse', 'reverse', 'decoy', 'random', 'shuffle']
for mod in mods:
if mod in protein:
if protein.endswith('_{}'.format(mod)):
return '_{}'.format(mod)
elif protein.endswith('{}'.format(mod)):
return mod
elif protein.startswith('{}_'.format(mod)):
return '{}_'.format(mod)
elif protein.startswith('{}'.format(mod)):
return mod
def get_description(record, rectype):
if rectype == 'ensembl':
desc_spl = [x.split(':') for x in record.description.split()]
try:
descix = [ix for ix, x in enumerate(desc_spl) if x[0] == 'description'][0]
except IndexError:
return 'NA'
desc = ' '.join([':'.join(x) for x in desc_spl[descix:]])[12:]
return desc
elif rectype == 'swiss':
desc = []
for part in record.description.split()[1:]:
if len(part.split('=')) > 1:
break
desc.append(part)
return ' '.join(desc)
def get_other_gene(record, fastadelim, genefield):
return record.description.split(fastadelim)[genefield]
def get_genes_pickfdr(fastafn, outputtype, fastadelim, genefield):
"""Called by protein FDR module for both ENSG and e.g. Uniprot"""
for rec in parse_fasta(fastafn):
rtype = get_record_type(rec)
if rtype == 'ensembl' and outputtype == 'ensg':
yield get_ensg(rec)
elif outputtype == 'genename':
yield get_symbol(rec, rtype, fastadelim, genefield)
def get_ensg(record):
fields = [x.split(':') for x in record.description.split()]
try:
return [x[1] for x in fields if x[0] == 'gene' and len(x) == 2][0]
except IndexError:
raise RuntimeError('ENSEMBL detected but cannot find gene ENSG in fasta')
def get_symbol(record, rectype, fastadelim, genefield):
if rectype == 'ensembl':
fields = [x.split(':') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'gene_symbol' and len(x) == 2]
elif rectype == 'swiss':
fields = [x.split('=') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'GN' and len(x) == 2]
elif fastadelim and fastadelim in record.description and genefield:
return record.description.split(fastadelim)[genefield]
else:
return 'NA'
try:
return sym[0]
except IndexError:
return 'NA'
def get_uniprot_evidence_level(record, rtype):
"""Returns uniprot protein existence evidence level for a fasta header.
Evidence levels are 1-5, but we return 5 - x since sorting still demands
that higher is better."""
if rtype != 'swiss':
return -1
for item in record.description.split():
item = item.split('=')
try:
if item[0] == 'PE' and len(item) == 2:
return 5 - int(item[1])
except IndexError:
continue
return -1
<｜fim▁end｜> | with open(fn) as fp:
for record in SeqIO.parse(fp, 'fasta'):
yield record |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by keeping only the last one.
"""
records = {acc: (rec, get_record_type(rec)) for acc, rec in
SeqIO.index(fastafn, 'fasta').items()}
proteins = ((x,) for x in records.keys())
sequences = ((acc, str(rec.seq)) for acc, (rec, rtype) in records.items())
desc = ((acc, get_description(rec, rtype)) for acc, (rec, rtype) in records.items() if rtype)
evid = ((acc, get_uniprot_evidence_level(rec, rtype)) for acc, (rec, rtype) in
records.items())
ensgs = [(get_ensg(rec), acc) for acc, (rec, rtype) in records.items()
if rtype == 'ensembl']
def sym_out():
symbols = ((get_symbol(rec, rtype, fastadelim, genefield), acc) for
acc, (rec, rtype) in records.items() if rtype)
othergene = ((get_other_gene(rec, fastadelim, genefield), acc) for acc, (rec, rtype) in records.items()
if not rtype and fastadelim and fastadelim in rec.description)
yield from symbols
yield from othergene
return proteins, sequences, desc, evid, ensgs, [x for x in sym_out()]
def parse_fasta(fn):
with open(fn) as fp:
for record in SeqIO.parse(fp, 'fasta'):
yield record
def get_record_type(record):
<|fim_middle|>
def get_decoy_mod_string(protein):
mods = ['tryp_reverse', 'reverse', 'decoy', 'random', 'shuffle']
for mod in mods:
if mod in protein:
if protein.endswith('_{}'.format(mod)):
return '_{}'.format(mod)
elif protein.endswith('{}'.format(mod)):
return mod
elif protein.startswith('{}_'.format(mod)):
return '{}_'.format(mod)
elif protein.startswith('{}'.format(mod)):
return mod
def get_description(record, rectype):
if rectype == 'ensembl':
desc_spl = [x.split(':') for x in record.description.split()]
try:
descix = [ix for ix, x in enumerate(desc_spl) if x[0] == 'description'][0]
except IndexError:
return 'NA'
desc = ' '.join([':'.join(x) for x in desc_spl[descix:]])[12:]
return desc
elif rectype == 'swiss':
desc = []
for part in record.description.split()[1:]:
if len(part.split('=')) > 1:
break
desc.append(part)
return ' '.join(desc)
def get_other_gene(record, fastadelim, genefield):
return record.description.split(fastadelim)[genefield]
def get_genes_pickfdr(fastafn, outputtype, fastadelim, genefield):
"""Called by protein FDR module for both ENSG and e.g. Uniprot"""
for rec in parse_fasta(fastafn):
rtype = get_record_type(rec)
if rtype == 'ensembl' and outputtype == 'ensg':
yield get_ensg(rec)
elif outputtype == 'genename':
yield get_symbol(rec, rtype, fastadelim, genefield)
def get_ensg(record):
fields = [x.split(':') for x in record.description.split()]
try:
return [x[1] for x in fields if x[0] == 'gene' and len(x) == 2][0]
except IndexError:
raise RuntimeError('ENSEMBL detected but cannot find gene ENSG in fasta')
def get_symbol(record, rectype, fastadelim, genefield):
if rectype == 'ensembl':
fields = [x.split(':') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'gene_symbol' and len(x) == 2]
elif rectype == 'swiss':
fields = [x.split('=') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'GN' and len(x) == 2]
elif fastadelim and fastadelim in record.description and genefield:
return record.description.split(fastadelim)[genefield]
else:
return 'NA'
try:
return sym[0]
except IndexError:
return 'NA'
def get_uniprot_evidence_level(record, rtype):
"""Returns uniprot protein existence evidence level for a fasta header.
Evidence levels are 1-5, but we return 5 - x since sorting still demands
that higher is better."""
if rtype != 'swiss':
return -1
for item in record.description.split():
item = item.split('=')
try:
if item[0] == 'PE' and len(item) == 2:
return 5 - int(item[1])
except IndexError:
continue
return -1
<｜fim▁end｜> | dmod = get_decoy_mod_string(record.id)
test_name = record.id
if dmod is not None:
test_name = record.id.replace(dmod, '')
if test_name.split('|')[0] in ['sp', 'tr']:
return 'swiss'
elif test_name[:3] == 'ENS':
return 'ensembl'
else:
return False |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by keeping only the last one.
"""
records = {acc: (rec, get_record_type(rec)) for acc, rec in
SeqIO.index(fastafn, 'fasta').items()}
proteins = ((x,) for x in records.keys())
sequences = ((acc, str(rec.seq)) for acc, (rec, rtype) in records.items())
desc = ((acc, get_description(rec, rtype)) for acc, (rec, rtype) in records.items() if rtype)
evid = ((acc, get_uniprot_evidence_level(rec, rtype)) for acc, (rec, rtype) in
records.items())
ensgs = [(get_ensg(rec), acc) for acc, (rec, rtype) in records.items()
if rtype == 'ensembl']
def sym_out():
symbols = ((get_symbol(rec, rtype, fastadelim, genefield), acc) for
acc, (rec, rtype) in records.items() if rtype)
othergene = ((get_other_gene(rec, fastadelim, genefield), acc) for acc, (rec, rtype) in records.items()
if not rtype and fastadelim and fastadelim in rec.description)
yield from symbols
yield from othergene
return proteins, sequences, desc, evid, ensgs, [x for x in sym_out()]
def parse_fasta(fn):
with open(fn) as fp:
for record in SeqIO.parse(fp, 'fasta'):
yield record
def get_record_type(record):
dmod = get_decoy_mod_string(record.id)
test_name = record.id
if dmod is not None:
test_name = record.id.replace(dmod, '')
if test_name.split('|')[0] in ['sp', 'tr']:
return 'swiss'
elif test_name[:3] == 'ENS':
return 'ensembl'
else:
return False
def get_decoy_mod_string(protein):
<|fim_middle|>
def get_description(record, rectype):
if rectype == 'ensembl':
desc_spl = [x.split(':') for x in record.description.split()]
try:
descix = [ix for ix, x in enumerate(desc_spl) if x[0] == 'description'][0]
except IndexError:
return 'NA'
desc = ' '.join([':'.join(x) for x in desc_spl[descix:]])[12:]
return desc
elif rectype == 'swiss':
desc = []
for part in record.description.split()[1:]:
if len(part.split('=')) > 1:
break
desc.append(part)
return ' '.join(desc)
def get_other_gene(record, fastadelim, genefield):
return record.description.split(fastadelim)[genefield]
def get_genes_pickfdr(fastafn, outputtype, fastadelim, genefield):
"""Called by protein FDR module for both ENSG and e.g. Uniprot"""
for rec in parse_fasta(fastafn):
rtype = get_record_type(rec)
if rtype == 'ensembl' and outputtype == 'ensg':
yield get_ensg(rec)
elif outputtype == 'genename':
yield get_symbol(rec, rtype, fastadelim, genefield)
def get_ensg(record):
fields = [x.split(':') for x in record.description.split()]
try:
return [x[1] for x in fields if x[0] == 'gene' and len(x) == 2][0]
except IndexError:
raise RuntimeError('ENSEMBL detected but cannot find gene ENSG in fasta')
def get_symbol(record, rectype, fastadelim, genefield):
if rectype == 'ensembl':
fields = [x.split(':') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'gene_symbol' and len(x) == 2]
elif rectype == 'swiss':
fields = [x.split('=') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'GN' and len(x) == 2]
elif fastadelim and fastadelim in record.description and genefield:
return record.description.split(fastadelim)[genefield]
else:
return 'NA'
try:
return sym[0]
except IndexError:
return 'NA'
def get_uniprot_evidence_level(record, rtype):
"""Returns uniprot protein existence evidence level for a fasta header.
Evidence levels are 1-5, but we return 5 - x since sorting still demands
that higher is better."""
if rtype != 'swiss':
return -1
for item in record.description.split():
item = item.split('=')
try:
if item[0] == 'PE' and len(item) == 2:
return 5 - int(item[1])
except IndexError:
continue
return -1
<｜fim▁end｜> | mods = ['tryp_reverse', 'reverse', 'decoy', 'random', 'shuffle']
for mod in mods:
if mod in protein:
if protein.endswith('_{}'.format(mod)):
return '_{}'.format(mod)
elif protein.endswith('{}'.format(mod)):
return mod
elif protein.startswith('{}_'.format(mod)):
return '{}_'.format(mod)
elif protein.startswith('{}'.format(mod)):
return mod |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by keeping only the last one.
"""
records = {acc: (rec, get_record_type(rec)) for acc, rec in
SeqIO.index(fastafn, 'fasta').items()}
proteins = ((x,) for x in records.keys())
sequences = ((acc, str(rec.seq)) for acc, (rec, rtype) in records.items())
desc = ((acc, get_description(rec, rtype)) for acc, (rec, rtype) in records.items() if rtype)
evid = ((acc, get_uniprot_evidence_level(rec, rtype)) for acc, (rec, rtype) in
records.items())
ensgs = [(get_ensg(rec), acc) for acc, (rec, rtype) in records.items()
if rtype == 'ensembl']
def sym_out():
symbols = ((get_symbol(rec, rtype, fastadelim, genefield), acc) for
acc, (rec, rtype) in records.items() if rtype)
othergene = ((get_other_gene(rec, fastadelim, genefield), acc) for acc, (rec, rtype) in records.items()
if not rtype and fastadelim and fastadelim in rec.description)
yield from symbols
yield from othergene
return proteins, sequences, desc, evid, ensgs, [x for x in sym_out()]
def parse_fasta(fn):
with open(fn) as fp:
for record in SeqIO.parse(fp, 'fasta'):
yield record
def get_record_type(record):
dmod = get_decoy_mod_string(record.id)
test_name = record.id
if dmod is not None:
test_name = record.id.replace(dmod, '')
if test_name.split('|')[0] in ['sp', 'tr']:
return 'swiss'
elif test_name[:3] == 'ENS':
return 'ensembl'
else:
return False
def get_decoy_mod_string(protein):
mods = ['tryp_reverse', 'reverse', 'decoy', 'random', 'shuffle']
for mod in mods:
if mod in protein:
if protein.endswith('_{}'.format(mod)):
return '_{}'.format(mod)
elif protein.endswith('{}'.format(mod)):
return mod
elif protein.startswith('{}_'.format(mod)):
return '{}_'.format(mod)
elif protein.startswith('{}'.format(mod)):
return mod
def get_description(record, rectype):
<|fim_middle|>
def get_other_gene(record, fastadelim, genefield):
return record.description.split(fastadelim)[genefield]
def get_genes_pickfdr(fastafn, outputtype, fastadelim, genefield):
"""Called by protein FDR module for both ENSG and e.g. Uniprot"""
for rec in parse_fasta(fastafn):
rtype = get_record_type(rec)
if rtype == 'ensembl' and outputtype == 'ensg':
yield get_ensg(rec)
elif outputtype == 'genename':
yield get_symbol(rec, rtype, fastadelim, genefield)
def get_ensg(record):
fields = [x.split(':') for x in record.description.split()]
try:
return [x[1] for x in fields if x[0] == 'gene' and len(x) == 2][0]
except IndexError:
raise RuntimeError('ENSEMBL detected but cannot find gene ENSG in fasta')
def get_symbol(record, rectype, fastadelim, genefield):
if rectype == 'ensembl':
fields = [x.split(':') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'gene_symbol' and len(x) == 2]
elif rectype == 'swiss':
fields = [x.split('=') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'GN' and len(x) == 2]
elif fastadelim and fastadelim in record.description and genefield:
return record.description.split(fastadelim)[genefield]
else:
return 'NA'
try:
return sym[0]
except IndexError:
return 'NA'
def get_uniprot_evidence_level(record, rtype):
"""Returns uniprot protein existence evidence level for a fasta header.
Evidence levels are 1-5, but we return 5 - x since sorting still demands
that higher is better."""
if rtype != 'swiss':
return -1
for item in record.description.split():
item = item.split('=')
try:
if item[0] == 'PE' and len(item) == 2:
return 5 - int(item[1])
except IndexError:
continue
return -1
<｜fim▁end｜> | if rectype == 'ensembl':
desc_spl = [x.split(':') for x in record.description.split()]
try:
descix = [ix for ix, x in enumerate(desc_spl) if x[0] == 'description'][0]
except IndexError:
return 'NA'
desc = ' '.join([':'.join(x) for x in desc_spl[descix:]])[12:]
return desc
elif rectype == 'swiss':
desc = []
for part in record.description.split()[1:]:
if len(part.split('=')) > 1:
break
desc.append(part)
return ' '.join(desc) |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by keeping only the last one.
"""
records = {acc: (rec, get_record_type(rec)) for acc, rec in
SeqIO.index(fastafn, 'fasta').items()}
proteins = ((x,) for x in records.keys())
sequences = ((acc, str(rec.seq)) for acc, (rec, rtype) in records.items())
desc = ((acc, get_description(rec, rtype)) for acc, (rec, rtype) in records.items() if rtype)
evid = ((acc, get_uniprot_evidence_level(rec, rtype)) for acc, (rec, rtype) in
records.items())
ensgs = [(get_ensg(rec), acc) for acc, (rec, rtype) in records.items()
if rtype == 'ensembl']
def sym_out():
symbols = ((get_symbol(rec, rtype, fastadelim, genefield), acc) for
acc, (rec, rtype) in records.items() if rtype)
othergene = ((get_other_gene(rec, fastadelim, genefield), acc) for acc, (rec, rtype) in records.items()
if not rtype and fastadelim and fastadelim in rec.description)
yield from symbols
yield from othergene
return proteins, sequences, desc, evid, ensgs, [x for x in sym_out()]
def parse_fasta(fn):
with open(fn) as fp:
for record in SeqIO.parse(fp, 'fasta'):
yield record
def get_record_type(record):
dmod = get_decoy_mod_string(record.id)
test_name = record.id
if dmod is not None:
test_name = record.id.replace(dmod, '')
if test_name.split('|')[0] in ['sp', 'tr']:
return 'swiss'
elif test_name[:3] == 'ENS':
return 'ensembl'
else:
return False
def get_decoy_mod_string(protein):
mods = ['tryp_reverse', 'reverse', 'decoy', 'random', 'shuffle']
for mod in mods:
if mod in protein:
if protein.endswith('_{}'.format(mod)):
return '_{}'.format(mod)
elif protein.endswith('{}'.format(mod)):
return mod
elif protein.startswith('{}_'.format(mod)):
return '{}_'.format(mod)
elif protein.startswith('{}'.format(mod)):
return mod
def get_description(record, rectype):
if rectype == 'ensembl':
desc_spl = [x.split(':') for x in record.description.split()]
try:
descix = [ix for ix, x in enumerate(desc_spl) if x[0] == 'description'][0]
except IndexError:
return 'NA'
desc = ' '.join([':'.join(x) for x in desc_spl[descix:]])[12:]
return desc
elif rectype == 'swiss':
desc = []
for part in record.description.split()[1:]:
if len(part.split('=')) > 1:
break
desc.append(part)
return ' '.join(desc)
def get_other_gene(record, fastadelim, genefield):
<|fim_middle|>
def get_genes_pickfdr(fastafn, outputtype, fastadelim, genefield):
"""Called by protein FDR module for both ENSG and e.g. Uniprot"""
for rec in parse_fasta(fastafn):
rtype = get_record_type(rec)
if rtype == 'ensembl' and outputtype == 'ensg':
yield get_ensg(rec)
elif outputtype == 'genename':
yield get_symbol(rec, rtype, fastadelim, genefield)
def get_ensg(record):
fields = [x.split(':') for x in record.description.split()]
try:
return [x[1] for x in fields if x[0] == 'gene' and len(x) == 2][0]
except IndexError:
raise RuntimeError('ENSEMBL detected but cannot find gene ENSG in fasta')
def get_symbol(record, rectype, fastadelim, genefield):
if rectype == 'ensembl':
fields = [x.split(':') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'gene_symbol' and len(x) == 2]
elif rectype == 'swiss':
fields = [x.split('=') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'GN' and len(x) == 2]
elif fastadelim and fastadelim in record.description and genefield:
return record.description.split(fastadelim)[genefield]
else:
return 'NA'
try:
return sym[0]
except IndexError:
return 'NA'
def get_uniprot_evidence_level(record, rtype):
"""Returns uniprot protein existence evidence level for a fasta header.
Evidence levels are 1-5, but we return 5 - x since sorting still demands
that higher is better."""
if rtype != 'swiss':
return -1
for item in record.description.split():
item = item.split('=')
try:
if item[0] == 'PE' and len(item) == 2:
return 5 - int(item[1])
except IndexError:
continue
return -1
<｜fim▁end｜> | return record.description.split(fastadelim)[genefield] |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by keeping only the last one.
"""
records = {acc: (rec, get_record_type(rec)) for acc, rec in
SeqIO.index(fastafn, 'fasta').items()}
proteins = ((x,) for x in records.keys())
sequences = ((acc, str(rec.seq)) for acc, (rec, rtype) in records.items())
desc = ((acc, get_description(rec, rtype)) for acc, (rec, rtype) in records.items() if rtype)
evid = ((acc, get_uniprot_evidence_level(rec, rtype)) for acc, (rec, rtype) in
records.items())
ensgs = [(get_ensg(rec), acc) for acc, (rec, rtype) in records.items()
if rtype == 'ensembl']
def sym_out():
symbols = ((get_symbol(rec, rtype, fastadelim, genefield), acc) for
acc, (rec, rtype) in records.items() if rtype)
othergene = ((get_other_gene(rec, fastadelim, genefield), acc) for acc, (rec, rtype) in records.items()
if not rtype and fastadelim and fastadelim in rec.description)
yield from symbols
yield from othergene
return proteins, sequences, desc, evid, ensgs, [x for x in sym_out()]
def parse_fasta(fn):
with open(fn) as fp:
for record in SeqIO.parse(fp, 'fasta'):
yield record
def get_record_type(record):
dmod = get_decoy_mod_string(record.id)
test_name = record.id
if dmod is not None:
test_name = record.id.replace(dmod, '')
if test_name.split('|')[0] in ['sp', 'tr']:
return 'swiss'
elif test_name[:3] == 'ENS':
return 'ensembl'
else:
return False
def get_decoy_mod_string(protein):
mods = ['tryp_reverse', 'reverse', 'decoy', 'random', 'shuffle']
for mod in mods:
if mod in protein:
if protein.endswith('_{}'.format(mod)):
return '_{}'.format(mod)
elif protein.endswith('{}'.format(mod)):
return mod
elif protein.startswith('{}_'.format(mod)):
return '{}_'.format(mod)
elif protein.startswith('{}'.format(mod)):
return mod
def get_description(record, rectype):
if rectype == 'ensembl':
desc_spl = [x.split(':') for x in record.description.split()]
try:
descix = [ix for ix, x in enumerate(desc_spl) if x[0] == 'description'][0]
except IndexError:
return 'NA'
desc = ' '.join([':'.join(x) for x in desc_spl[descix:]])[12:]
return desc
elif rectype == 'swiss':
desc = []
for part in record.description.split()[1:]:
if len(part.split('=')) > 1:
break
desc.append(part)
return ' '.join(desc)
def get_other_gene(record, fastadelim, genefield):
return record.description.split(fastadelim)[genefield]
def get_genes_pickfdr(fastafn, outputtype, fastadelim, genefield):
<|fim_middle|>
def get_ensg(record):
fields = [x.split(':') for x in record.description.split()]
try:
return [x[1] for x in fields if x[0] == 'gene' and len(x) == 2][0]
except IndexError:
raise RuntimeError('ENSEMBL detected but cannot find gene ENSG in fasta')
def get_symbol(record, rectype, fastadelim, genefield):
if rectype == 'ensembl':
fields = [x.split(':') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'gene_symbol' and len(x) == 2]
elif rectype == 'swiss':
fields = [x.split('=') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'GN' and len(x) == 2]
elif fastadelim and fastadelim in record.description and genefield:
return record.description.split(fastadelim)[genefield]
else:
return 'NA'
try:
return sym[0]
except IndexError:
return 'NA'
def get_uniprot_evidence_level(record, rtype):
"""Returns uniprot protein existence evidence level for a fasta header.
Evidence levels are 1-5, but we return 5 - x since sorting still demands
that higher is better."""
if rtype != 'swiss':
return -1
for item in record.description.split():
item = item.split('=')
try:
if item[0] == 'PE' and len(item) == 2:
return 5 - int(item[1])
except IndexError:
continue
return -1
<｜fim▁end｜> | """Called by protein FDR module for both ENSG and e.g. Uniprot"""
for rec in parse_fasta(fastafn):
rtype = get_record_type(rec)
if rtype == 'ensembl' and outputtype == 'ensg':
yield get_ensg(rec)
elif outputtype == 'genename':
yield get_symbol(rec, rtype, fastadelim, genefield) |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by keeping only the last one.
"""
records = {acc: (rec, get_record_type(rec)) for acc, rec in
SeqIO.index(fastafn, 'fasta').items()}
proteins = ((x,) for x in records.keys())
sequences = ((acc, str(rec.seq)) for acc, (rec, rtype) in records.items())
desc = ((acc, get_description(rec, rtype)) for acc, (rec, rtype) in records.items() if rtype)
evid = ((acc, get_uniprot_evidence_level(rec, rtype)) for acc, (rec, rtype) in
records.items())
ensgs = [(get_ensg(rec), acc) for acc, (rec, rtype) in records.items()
if rtype == 'ensembl']
def sym_out():
symbols = ((get_symbol(rec, rtype, fastadelim, genefield), acc) for
acc, (rec, rtype) in records.items() if rtype)
othergene = ((get_other_gene(rec, fastadelim, genefield), acc) for acc, (rec, rtype) in records.items()
if not rtype and fastadelim and fastadelim in rec.description)
yield from symbols
yield from othergene
return proteins, sequences, desc, evid, ensgs, [x for x in sym_out()]
def parse_fasta(fn):
with open(fn) as fp:
for record in SeqIO.parse(fp, 'fasta'):
yield record
def get_record_type(record):
dmod = get_decoy_mod_string(record.id)
test_name = record.id
if dmod is not None:
test_name = record.id.replace(dmod, '')
if test_name.split('|')[0] in ['sp', 'tr']:
return 'swiss'
elif test_name[:3] == 'ENS':
return 'ensembl'
else:
return False
def get_decoy_mod_string(protein):
mods = ['tryp_reverse', 'reverse', 'decoy', 'random', 'shuffle']
for mod in mods:
if mod in protein:
if protein.endswith('_{}'.format(mod)):
return '_{}'.format(mod)
elif protein.endswith('{}'.format(mod)):
return mod
elif protein.startswith('{}_'.format(mod)):
return '{}_'.format(mod)
elif protein.startswith('{}'.format(mod)):
return mod
def get_description(record, rectype):
if rectype == 'ensembl':
desc_spl = [x.split(':') for x in record.description.split()]
try:
descix = [ix for ix, x in enumerate(desc_spl) if x[0] == 'description'][0]
except IndexError:
return 'NA'
desc = ' '.join([':'.join(x) for x in desc_spl[descix:]])[12:]
return desc
elif rectype == 'swiss':
desc = []
for part in record.description.split()[1:]:
if len(part.split('=')) > 1:
break
desc.append(part)
return ' '.join(desc)
def get_other_gene(record, fastadelim, genefield):
return record.description.split(fastadelim)[genefield]
def get_genes_pickfdr(fastafn, outputtype, fastadelim, genefield):
"""Called by protein FDR module for both ENSG and e.g. Uniprot"""
for rec in parse_fasta(fastafn):
rtype = get_record_type(rec)
if rtype == 'ensembl' and outputtype == 'ensg':
yield get_ensg(rec)
elif outputtype == 'genename':
yield get_symbol(rec, rtype, fastadelim, genefield)
def get_ensg(record):
<|fim_middle|>
def get_symbol(record, rectype, fastadelim, genefield):
if rectype == 'ensembl':
fields = [x.split(':') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'gene_symbol' and len(x) == 2]
elif rectype == 'swiss':
fields = [x.split('=') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'GN' and len(x) == 2]
elif fastadelim and fastadelim in record.description and genefield:
return record.description.split(fastadelim)[genefield]
else:
return 'NA'
try:
return sym[0]
except IndexError:
return 'NA'
def get_uniprot_evidence_level(record, rtype):
"""Returns uniprot protein existence evidence level for a fasta header.
Evidence levels are 1-5, but we return 5 - x since sorting still demands
that higher is better."""
if rtype != 'swiss':
return -1
for item in record.description.split():
item = item.split('=')
try:
if item[0] == 'PE' and len(item) == 2:
return 5 - int(item[1])
except IndexError:
continue
return -1
<｜fim▁end｜> | fields = [x.split(':') for x in record.description.split()]
try:
return [x[1] for x in fields if x[0] == 'gene' and len(x) == 2][0]
except IndexError:
raise RuntimeError('ENSEMBL detected but cannot find gene ENSG in fasta') |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by keeping only the last one.
"""
records = {acc: (rec, get_record_type(rec)) for acc, rec in
SeqIO.index(fastafn, 'fasta').items()}
proteins = ((x,) for x in records.keys())
sequences = ((acc, str(rec.seq)) for acc, (rec, rtype) in records.items())
desc = ((acc, get_description(rec, rtype)) for acc, (rec, rtype) in records.items() if rtype)
evid = ((acc, get_uniprot_evidence_level(rec, rtype)) for acc, (rec, rtype) in
records.items())
ensgs = [(get_ensg(rec), acc) for acc, (rec, rtype) in records.items()
if rtype == 'ensembl']
def sym_out():
symbols = ((get_symbol(rec, rtype, fastadelim, genefield), acc) for
acc, (rec, rtype) in records.items() if rtype)
othergene = ((get_other_gene(rec, fastadelim, genefield), acc) for acc, (rec, rtype) in records.items()
if not rtype and fastadelim and fastadelim in rec.description)
yield from symbols
yield from othergene
return proteins, sequences, desc, evid, ensgs, [x for x in sym_out()]
def parse_fasta(fn):
with open(fn) as fp:
for record in SeqIO.parse(fp, 'fasta'):
yield record
def get_record_type(record):
dmod = get_decoy_mod_string(record.id)
test_name = record.id
if dmod is not None:
test_name = record.id.replace(dmod, '')
if test_name.split('|')[0] in ['sp', 'tr']:
return 'swiss'
elif test_name[:3] == 'ENS':
return 'ensembl'
else:
return False
def get_decoy_mod_string(protein):
mods = ['tryp_reverse', 'reverse', 'decoy', 'random', 'shuffle']
for mod in mods:
if mod in protein:
if protein.endswith('_{}'.format(mod)):
return '_{}'.format(mod)
elif protein.endswith('{}'.format(mod)):
return mod
elif protein.startswith('{}_'.format(mod)):
return '{}_'.format(mod)
elif protein.startswith('{}'.format(mod)):
return mod
def get_description(record, rectype):
if rectype == 'ensembl':
desc_spl = [x.split(':') for x in record.description.split()]
try:
descix = [ix for ix, x in enumerate(desc_spl) if x[0] == 'description'][0]
except IndexError:
return 'NA'
desc = ' '.join([':'.join(x) for x in desc_spl[descix:]])[12:]
return desc
elif rectype == 'swiss':
desc = []
for part in record.description.split()[1:]:
if len(part.split('=')) > 1:
break
desc.append(part)
return ' '.join(desc)
def get_other_gene(record, fastadelim, genefield):
return record.description.split(fastadelim)[genefield]
def get_genes_pickfdr(fastafn, outputtype, fastadelim, genefield):
"""Called by protein FDR module for both ENSG and e.g. Uniprot"""
for rec in parse_fasta(fastafn):
rtype = get_record_type(rec)
if rtype == 'ensembl' and outputtype == 'ensg':
yield get_ensg(rec)
elif outputtype == 'genename':
yield get_symbol(rec, rtype, fastadelim, genefield)
def get_ensg(record):
fields = [x.split(':') for x in record.description.split()]
try:
return [x[1] for x in fields if x[0] == 'gene' and len(x) == 2][0]
except IndexError:
raise RuntimeError('ENSEMBL detected but cannot find gene ENSG in fasta')
def get_symbol(record, rectype, fastadelim, genefield):
<|fim_middle|>
def get_uniprot_evidence_level(record, rtype):
"""Returns uniprot protein existence evidence level for a fasta header.
Evidence levels are 1-5, but we return 5 - x since sorting still demands
that higher is better."""
if rtype != 'swiss':
return -1
for item in record.description.split():
item = item.split('=')
try:
if item[0] == 'PE' and len(item) == 2:
return 5 - int(item[1])
except IndexError:
continue
return -1
<｜fim▁end｜> | if rectype == 'ensembl':
fields = [x.split(':') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'gene_symbol' and len(x) == 2]
elif rectype == 'swiss':
fields = [x.split('=') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'GN' and len(x) == 2]
elif fastadelim and fastadelim in record.description and genefield:
return record.description.split(fastadelim)[genefield]
else:
return 'NA'
try:
return sym[0]
except IndexError:
return 'NA' |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by keeping only the last one.
"""
records = {acc: (rec, get_record_type(rec)) for acc, rec in
SeqIO.index(fastafn, 'fasta').items()}
proteins = ((x,) for x in records.keys())
sequences = ((acc, str(rec.seq)) for acc, (rec, rtype) in records.items())
desc = ((acc, get_description(rec, rtype)) for acc, (rec, rtype) in records.items() if rtype)
evid = ((acc, get_uniprot_evidence_level(rec, rtype)) for acc, (rec, rtype) in
records.items())
ensgs = [(get_ensg(rec), acc) for acc, (rec, rtype) in records.items()
if rtype == 'ensembl']
def sym_out():
symbols = ((get_symbol(rec, rtype, fastadelim, genefield), acc) for
acc, (rec, rtype) in records.items() if rtype)
othergene = ((get_other_gene(rec, fastadelim, genefield), acc) for acc, (rec, rtype) in records.items()
if not rtype and fastadelim and fastadelim in rec.description)
yield from symbols
yield from othergene
return proteins, sequences, desc, evid, ensgs, [x for x in sym_out()]
def parse_fasta(fn):
with open(fn) as fp:
for record in SeqIO.parse(fp, 'fasta'):
yield record
def get_record_type(record):
dmod = get_decoy_mod_string(record.id)
test_name = record.id
if dmod is not None:
test_name = record.id.replace(dmod, '')
if test_name.split('|')[0] in ['sp', 'tr']:
return 'swiss'
elif test_name[:3] == 'ENS':
return 'ensembl'
else:
return False
def get_decoy_mod_string(protein):
mods = ['tryp_reverse', 'reverse', 'decoy', 'random', 'shuffle']
for mod in mods:
if mod in protein:
if protein.endswith('_{}'.format(mod)):
return '_{}'.format(mod)
elif protein.endswith('{}'.format(mod)):
return mod
elif protein.startswith('{}_'.format(mod)):
return '{}_'.format(mod)
elif protein.startswith('{}'.format(mod)):
return mod
def get_description(record, rectype):
if rectype == 'ensembl':
desc_spl = [x.split(':') for x in record.description.split()]
try:
descix = [ix for ix, x in enumerate(desc_spl) if x[0] == 'description'][0]
except IndexError:
return 'NA'
desc = ' '.join([':'.join(x) for x in desc_spl[descix:]])[12:]
return desc
elif rectype == 'swiss':
desc = []
for part in record.description.split()[1:]:
if len(part.split('=')) > 1:
break
desc.append(part)
return ' '.join(desc)
def get_other_gene(record, fastadelim, genefield):
return record.description.split(fastadelim)[genefield]
def get_genes_pickfdr(fastafn, outputtype, fastadelim, genefield):
"""Called by protein FDR module for both ENSG and e.g. Uniprot"""
for rec in parse_fasta(fastafn):
rtype = get_record_type(rec)
if rtype == 'ensembl' and outputtype == 'ensg':
yield get_ensg(rec)
elif outputtype == 'genename':
yield get_symbol(rec, rtype, fastadelim, genefield)
def get_ensg(record):
fields = [x.split(':') for x in record.description.split()]
try:
return [x[1] for x in fields if x[0] == 'gene' and len(x) == 2][0]
except IndexError:
raise RuntimeError('ENSEMBL detected but cannot find gene ENSG in fasta')
def get_symbol(record, rectype, fastadelim, genefield):
if rectype == 'ensembl':
fields = [x.split(':') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'gene_symbol' and len(x) == 2]
elif rectype == 'swiss':
fields = [x.split('=') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'GN' and len(x) == 2]
elif fastadelim and fastadelim in record.description and genefield:
return record.description.split(fastadelim)[genefield]
else:
return 'NA'
try:
return sym[0]
except IndexError:
return 'NA'
def get_uniprot_evidence_level(record, rtype):
<|fim_middle|>
<｜fim▁end｜> | """Returns uniprot protein existence evidence level for a fasta header.
Evidence levels are 1-5, but we return 5 - x since sorting still demands
that higher is better."""
if rtype != 'swiss':
return -1
for item in record.description.split():
item = item.split('=')
try:
if item[0] == 'PE' and len(item) == 2:
return 5 - int(item[1])
except IndexError:
continue
return -1 |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by keeping only the last one.
"""
records = {acc: (rec, get_record_type(rec)) for acc, rec in
SeqIO.index(fastafn, 'fasta').items()}
proteins = ((x,) for x in records.keys())
sequences = ((acc, str(rec.seq)) for acc, (rec, rtype) in records.items())
desc = ((acc, get_description(rec, rtype)) for acc, (rec, rtype) in records.items() if rtype)
evid = ((acc, get_uniprot_evidence_level(rec, rtype)) for acc, (rec, rtype) in
records.items())
ensgs = [(get_ensg(rec), acc) for acc, (rec, rtype) in records.items()
if rtype == 'ensembl']
def sym_out():
symbols = ((get_symbol(rec, rtype, fastadelim, genefield), acc) for
acc, (rec, rtype) in records.items() if rtype)
othergene = ((get_other_gene(rec, fastadelim, genefield), acc) for acc, (rec, rtype) in records.items()
if not rtype and fastadelim and fastadelim in rec.description)
yield from symbols
yield from othergene
return proteins, sequences, desc, evid, ensgs, [x for x in sym_out()]
def parse_fasta(fn):
with open(fn) as fp:
for record in SeqIO.parse(fp, 'fasta'):
yield record
def get_record_type(record):
dmod = get_decoy_mod_string(record.id)
test_name = record.id
if dmod is not None:
<|fim_middle|>
if test_name.split('|')[0] in ['sp', 'tr']:
return 'swiss'
elif test_name[:3] == 'ENS':
return 'ensembl'
else:
return False
def get_decoy_mod_string(protein):
mods = ['tryp_reverse', 'reverse', 'decoy', 'random', 'shuffle']
for mod in mods:
if mod in protein:
if protein.endswith('_{}'.format(mod)):
return '_{}'.format(mod)
elif protein.endswith('{}'.format(mod)):
return mod
elif protein.startswith('{}_'.format(mod)):
return '{}_'.format(mod)
elif protein.startswith('{}'.format(mod)):
return mod
def get_description(record, rectype):
if rectype == 'ensembl':
desc_spl = [x.split(':') for x in record.description.split()]
try:
descix = [ix for ix, x in enumerate(desc_spl) if x[0] == 'description'][0]
except IndexError:
return 'NA'
desc = ' '.join([':'.join(x) for x in desc_spl[descix:]])[12:]
return desc
elif rectype == 'swiss':
desc = []
for part in record.description.split()[1:]:
if len(part.split('=')) > 1:
break
desc.append(part)
return ' '.join(desc)
def get_other_gene(record, fastadelim, genefield):
return record.description.split(fastadelim)[genefield]
def get_genes_pickfdr(fastafn, outputtype, fastadelim, genefield):
"""Called by protein FDR module for both ENSG and e.g. Uniprot"""
for rec in parse_fasta(fastafn):
rtype = get_record_type(rec)
if rtype == 'ensembl' and outputtype == 'ensg':
yield get_ensg(rec)
elif outputtype == 'genename':
yield get_symbol(rec, rtype, fastadelim, genefield)
def get_ensg(record):
fields = [x.split(':') for x in record.description.split()]
try:
return [x[1] for x in fields if x[0] == 'gene' and len(x) == 2][0]
except IndexError:
raise RuntimeError('ENSEMBL detected but cannot find gene ENSG in fasta')
def get_symbol(record, rectype, fastadelim, genefield):
if rectype == 'ensembl':
fields = [x.split(':') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'gene_symbol' and len(x) == 2]
elif rectype == 'swiss':
fields = [x.split('=') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'GN' and len(x) == 2]
elif fastadelim and fastadelim in record.description and genefield:
return record.description.split(fastadelim)[genefield]
else:
return 'NA'
try:
return sym[0]
except IndexError:
return 'NA'
def get_uniprot_evidence_level(record, rtype):
"""Returns uniprot protein existence evidence level for a fasta header.
Evidence levels are 1-5, but we return 5 - x since sorting still demands
that higher is better."""
if rtype != 'swiss':
return -1
for item in record.description.split():
item = item.split('=')
try:
if item[0] == 'PE' and len(item) == 2:
return 5 - int(item[1])
except IndexError:
continue
return -1
<｜fim▁end｜> | test_name = record.id.replace(dmod, '') |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by keeping only the last one.
"""
records = {acc: (rec, get_record_type(rec)) for acc, rec in
SeqIO.index(fastafn, 'fasta').items()}
proteins = ((x,) for x in records.keys())
sequences = ((acc, str(rec.seq)) for acc, (rec, rtype) in records.items())
desc = ((acc, get_description(rec, rtype)) for acc, (rec, rtype) in records.items() if rtype)
evid = ((acc, get_uniprot_evidence_level(rec, rtype)) for acc, (rec, rtype) in
records.items())
ensgs = [(get_ensg(rec), acc) for acc, (rec, rtype) in records.items()
if rtype == 'ensembl']
def sym_out():
symbols = ((get_symbol(rec, rtype, fastadelim, genefield), acc) for
acc, (rec, rtype) in records.items() if rtype)
othergene = ((get_other_gene(rec, fastadelim, genefield), acc) for acc, (rec, rtype) in records.items()
if not rtype and fastadelim and fastadelim in rec.description)
yield from symbols
yield from othergene
return proteins, sequences, desc, evid, ensgs, [x for x in sym_out()]
def parse_fasta(fn):
with open(fn) as fp:
for record in SeqIO.parse(fp, 'fasta'):
yield record
def get_record_type(record):
dmod = get_decoy_mod_string(record.id)
test_name = record.id
if dmod is not None:
test_name = record.id.replace(dmod, '')
if test_name.split('|')[0] in ['sp', 'tr']:
<|fim_middle|>
elif test_name[:3] == 'ENS':
return 'ensembl'
else:
return False
def get_decoy_mod_string(protein):
mods = ['tryp_reverse', 'reverse', 'decoy', 'random', 'shuffle']
for mod in mods:
if mod in protein:
if protein.endswith('_{}'.format(mod)):
return '_{}'.format(mod)
elif protein.endswith('{}'.format(mod)):
return mod
elif protein.startswith('{}_'.format(mod)):
return '{}_'.format(mod)
elif protein.startswith('{}'.format(mod)):
return mod
def get_description(record, rectype):
if rectype == 'ensembl':
desc_spl = [x.split(':') for x in record.description.split()]
try:
descix = [ix for ix, x in enumerate(desc_spl) if x[0] == 'description'][0]
except IndexError:
return 'NA'
desc = ' '.join([':'.join(x) for x in desc_spl[descix:]])[12:]
return desc
elif rectype == 'swiss':
desc = []
for part in record.description.split()[1:]:
if len(part.split('=')) > 1:
break
desc.append(part)
return ' '.join(desc)
def get_other_gene(record, fastadelim, genefield):
return record.description.split(fastadelim)[genefield]
def get_genes_pickfdr(fastafn, outputtype, fastadelim, genefield):
"""Called by protein FDR module for both ENSG and e.g. Uniprot"""
for rec in parse_fasta(fastafn):
rtype = get_record_type(rec)
if rtype == 'ensembl' and outputtype == 'ensg':
yield get_ensg(rec)
elif outputtype == 'genename':
yield get_symbol(rec, rtype, fastadelim, genefield)
def get_ensg(record):
fields = [x.split(':') for x in record.description.split()]
try:
return [x[1] for x in fields if x[0] == 'gene' and len(x) == 2][0]
except IndexError:
raise RuntimeError('ENSEMBL detected but cannot find gene ENSG in fasta')
def get_symbol(record, rectype, fastadelim, genefield):
if rectype == 'ensembl':
fields = [x.split(':') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'gene_symbol' and len(x) == 2]
elif rectype == 'swiss':
fields = [x.split('=') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'GN' and len(x) == 2]
elif fastadelim and fastadelim in record.description and genefield:
return record.description.split(fastadelim)[genefield]
else:
return 'NA'
try:
return sym[0]
except IndexError:
return 'NA'
def get_uniprot_evidence_level(record, rtype):
"""Returns uniprot protein existence evidence level for a fasta header.
Evidence levels are 1-5, but we return 5 - x since sorting still demands
that higher is better."""
if rtype != 'swiss':
return -1
for item in record.description.split():
item = item.split('=')
try:
if item[0] == 'PE' and len(item) == 2:
return 5 - int(item[1])
except IndexError:
continue
return -1
<｜fim▁end｜> | return 'swiss' |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by keeping only the last one.
"""
records = {acc: (rec, get_record_type(rec)) for acc, rec in
SeqIO.index(fastafn, 'fasta').items()}
proteins = ((x,) for x in records.keys())
sequences = ((acc, str(rec.seq)) for acc, (rec, rtype) in records.items())
desc = ((acc, get_description(rec, rtype)) for acc, (rec, rtype) in records.items() if rtype)
evid = ((acc, get_uniprot_evidence_level(rec, rtype)) for acc, (rec, rtype) in
records.items())
ensgs = [(get_ensg(rec), acc) for acc, (rec, rtype) in records.items()
if rtype == 'ensembl']
def sym_out():
symbols = ((get_symbol(rec, rtype, fastadelim, genefield), acc) for
acc, (rec, rtype) in records.items() if rtype)
othergene = ((get_other_gene(rec, fastadelim, genefield), acc) for acc, (rec, rtype) in records.items()
if not rtype and fastadelim and fastadelim in rec.description)
yield from symbols
yield from othergene
return proteins, sequences, desc, evid, ensgs, [x for x in sym_out()]
def parse_fasta(fn):
with open(fn) as fp:
for record in SeqIO.parse(fp, 'fasta'):
yield record
def get_record_type(record):
dmod = get_decoy_mod_string(record.id)
test_name = record.id
if dmod is not None:
test_name = record.id.replace(dmod, '')
if test_name.split('|')[0] in ['sp', 'tr']:
return 'swiss'
elif test_name[:3] == 'ENS':
<|fim_middle|>
else:
return False
def get_decoy_mod_string(protein):
mods = ['tryp_reverse', 'reverse', 'decoy', 'random', 'shuffle']
for mod in mods:
if mod in protein:
if protein.endswith('_{}'.format(mod)):
return '_{}'.format(mod)
elif protein.endswith('{}'.format(mod)):
return mod
elif protein.startswith('{}_'.format(mod)):
return '{}_'.format(mod)
elif protein.startswith('{}'.format(mod)):
return mod
def get_description(record, rectype):
if rectype == 'ensembl':
desc_spl = [x.split(':') for x in record.description.split()]
try:
descix = [ix for ix, x in enumerate(desc_spl) if x[0] == 'description'][0]
except IndexError:
return 'NA'
desc = ' '.join([':'.join(x) for x in desc_spl[descix:]])[12:]
return desc
elif rectype == 'swiss':
desc = []
for part in record.description.split()[1:]:
if len(part.split('=')) > 1:
break
desc.append(part)
return ' '.join(desc)
def get_other_gene(record, fastadelim, genefield):
return record.description.split(fastadelim)[genefield]
def get_genes_pickfdr(fastafn, outputtype, fastadelim, genefield):
"""Called by protein FDR module for both ENSG and e.g. Uniprot"""
for rec in parse_fasta(fastafn):
rtype = get_record_type(rec)
if rtype == 'ensembl' and outputtype == 'ensg':
yield get_ensg(rec)
elif outputtype == 'genename':
yield get_symbol(rec, rtype, fastadelim, genefield)
def get_ensg(record):
fields = [x.split(':') for x in record.description.split()]
try:
return [x[1] for x in fields if x[0] == 'gene' and len(x) == 2][0]
except IndexError:
raise RuntimeError('ENSEMBL detected but cannot find gene ENSG in fasta')
def get_symbol(record, rectype, fastadelim, genefield):
if rectype == 'ensembl':
fields = [x.split(':') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'gene_symbol' and len(x) == 2]
elif rectype == 'swiss':
fields = [x.split('=') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'GN' and len(x) == 2]
elif fastadelim and fastadelim in record.description and genefield:
return record.description.split(fastadelim)[genefield]
else:
return 'NA'
try:
return sym[0]
except IndexError:
return 'NA'
def get_uniprot_evidence_level(record, rtype):
"""Returns uniprot protein existence evidence level for a fasta header.
Evidence levels are 1-5, but we return 5 - x since sorting still demands
that higher is better."""
if rtype != 'swiss':
return -1
for item in record.description.split():
item = item.split('=')
try:
if item[0] == 'PE' and len(item) == 2:
return 5 - int(item[1])
except IndexError:
continue
return -1
<｜fim▁end｜> | return 'ensembl' |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by keeping only the last one.
"""
records = {acc: (rec, get_record_type(rec)) for acc, rec in
SeqIO.index(fastafn, 'fasta').items()}
proteins = ((x,) for x in records.keys())
sequences = ((acc, str(rec.seq)) for acc, (rec, rtype) in records.items())
desc = ((acc, get_description(rec, rtype)) for acc, (rec, rtype) in records.items() if rtype)
evid = ((acc, get_uniprot_evidence_level(rec, rtype)) for acc, (rec, rtype) in
records.items())
ensgs = [(get_ensg(rec), acc) for acc, (rec, rtype) in records.items()
if rtype == 'ensembl']
def sym_out():
symbols = ((get_symbol(rec, rtype, fastadelim, genefield), acc) for
acc, (rec, rtype) in records.items() if rtype)
othergene = ((get_other_gene(rec, fastadelim, genefield), acc) for acc, (rec, rtype) in records.items()
if not rtype and fastadelim and fastadelim in rec.description)
yield from symbols
yield from othergene
return proteins, sequences, desc, evid, ensgs, [x for x in sym_out()]
def parse_fasta(fn):
with open(fn) as fp:
for record in SeqIO.parse(fp, 'fasta'):
yield record
def get_record_type(record):
dmod = get_decoy_mod_string(record.id)
test_name = record.id
if dmod is not None:
test_name = record.id.replace(dmod, '')
if test_name.split('|')[0] in ['sp', 'tr']:
return 'swiss'
elif test_name[:3] == 'ENS':
return 'ensembl'
else:
<|fim_middle|>
def get_decoy_mod_string(protein):
mods = ['tryp_reverse', 'reverse', 'decoy', 'random', 'shuffle']
for mod in mods:
if mod in protein:
if protein.endswith('_{}'.format(mod)):
return '_{}'.format(mod)
elif protein.endswith('{}'.format(mod)):
return mod
elif protein.startswith('{}_'.format(mod)):
return '{}_'.format(mod)
elif protein.startswith('{}'.format(mod)):
return mod
def get_description(record, rectype):
if rectype == 'ensembl':
desc_spl = [x.split(':') for x in record.description.split()]
try:
descix = [ix for ix, x in enumerate(desc_spl) if x[0] == 'description'][0]
except IndexError:
return 'NA'
desc = ' '.join([':'.join(x) for x in desc_spl[descix:]])[12:]
return desc
elif rectype == 'swiss':
desc = []
for part in record.description.split()[1:]:
if len(part.split('=')) > 1:
break
desc.append(part)
return ' '.join(desc)
def get_other_gene(record, fastadelim, genefield):
return record.description.split(fastadelim)[genefield]
def get_genes_pickfdr(fastafn, outputtype, fastadelim, genefield):
"""Called by protein FDR module for both ENSG and e.g. Uniprot"""
for rec in parse_fasta(fastafn):
rtype = get_record_type(rec)
if rtype == 'ensembl' and outputtype == 'ensg':
yield get_ensg(rec)
elif outputtype == 'genename':
yield get_symbol(rec, rtype, fastadelim, genefield)
def get_ensg(record):
fields = [x.split(':') for x in record.description.split()]
try:
return [x[1] for x in fields if x[0] == 'gene' and len(x) == 2][0]
except IndexError:
raise RuntimeError('ENSEMBL detected but cannot find gene ENSG in fasta')
def get_symbol(record, rectype, fastadelim, genefield):
if rectype == 'ensembl':
fields = [x.split(':') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'gene_symbol' and len(x) == 2]
elif rectype == 'swiss':
fields = [x.split('=') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'GN' and len(x) == 2]
elif fastadelim and fastadelim in record.description and genefield:
return record.description.split(fastadelim)[genefield]
else:
return 'NA'
try:
return sym[0]
except IndexError:
return 'NA'
def get_uniprot_evidence_level(record, rtype):
"""Returns uniprot protein existence evidence level for a fasta header.
Evidence levels are 1-5, but we return 5 - x since sorting still demands
that higher is better."""
if rtype != 'swiss':
return -1
for item in record.description.split():
item = item.split('=')
try:
if item[0] == 'PE' and len(item) == 2:
return 5 - int(item[1])
except IndexError:
continue
return -1
<｜fim▁end｜> | return False |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by keeping only the last one.
"""
records = {acc: (rec, get_record_type(rec)) for acc, rec in
SeqIO.index(fastafn, 'fasta').items()}
proteins = ((x,) for x in records.keys())
sequences = ((acc, str(rec.seq)) for acc, (rec, rtype) in records.items())
desc = ((acc, get_description(rec, rtype)) for acc, (rec, rtype) in records.items() if rtype)
evid = ((acc, get_uniprot_evidence_level(rec, rtype)) for acc, (rec, rtype) in
records.items())
ensgs = [(get_ensg(rec), acc) for acc, (rec, rtype) in records.items()
if rtype == 'ensembl']
def sym_out():
symbols = ((get_symbol(rec, rtype, fastadelim, genefield), acc) for
acc, (rec, rtype) in records.items() if rtype)
othergene = ((get_other_gene(rec, fastadelim, genefield), acc) for acc, (rec, rtype) in records.items()
if not rtype and fastadelim and fastadelim in rec.description)
yield from symbols
yield from othergene
return proteins, sequences, desc, evid, ensgs, [x for x in sym_out()]
def parse_fasta(fn):
with open(fn) as fp:
for record in SeqIO.parse(fp, 'fasta'):
yield record
def get_record_type(record):
dmod = get_decoy_mod_string(record.id)
test_name = record.id
if dmod is not None:
test_name = record.id.replace(dmod, '')
if test_name.split('|')[0] in ['sp', 'tr']:
return 'swiss'
elif test_name[:3] == 'ENS':
return 'ensembl'
else:
return False
def get_decoy_mod_string(protein):
mods = ['tryp_reverse', 'reverse', 'decoy', 'random', 'shuffle']
for mod in mods:
if mod in protein:
<|fim_middle|>
def get_description(record, rectype):
if rectype == 'ensembl':
desc_spl = [x.split(':') for x in record.description.split()]
try:
descix = [ix for ix, x in enumerate(desc_spl) if x[0] == 'description'][0]
except IndexError:
return 'NA'
desc = ' '.join([':'.join(x) for x in desc_spl[descix:]])[12:]
return desc
elif rectype == 'swiss':
desc = []
for part in record.description.split()[1:]:
if len(part.split('=')) > 1:
break
desc.append(part)
return ' '.join(desc)
def get_other_gene(record, fastadelim, genefield):
return record.description.split(fastadelim)[genefield]
def get_genes_pickfdr(fastafn, outputtype, fastadelim, genefield):
"""Called by protein FDR module for both ENSG and e.g. Uniprot"""
for rec in parse_fasta(fastafn):
rtype = get_record_type(rec)
if rtype == 'ensembl' and outputtype == 'ensg':
yield get_ensg(rec)
elif outputtype == 'genename':
yield get_symbol(rec, rtype, fastadelim, genefield)
def get_ensg(record):
fields = [x.split(':') for x in record.description.split()]
try:
return [x[1] for x in fields if x[0] == 'gene' and len(x) == 2][0]
except IndexError:
raise RuntimeError('ENSEMBL detected but cannot find gene ENSG in fasta')
def get_symbol(record, rectype, fastadelim, genefield):
if rectype == 'ensembl':
fields = [x.split(':') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'gene_symbol' and len(x) == 2]
elif rectype == 'swiss':
fields = [x.split('=') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'GN' and len(x) == 2]
elif fastadelim and fastadelim in record.description and genefield:
return record.description.split(fastadelim)[genefield]
else:
return 'NA'
try:
return sym[0]
except IndexError:
return 'NA'
def get_uniprot_evidence_level(record, rtype):
"""Returns uniprot protein existence evidence level for a fasta header.
Evidence levels are 1-5, but we return 5 - x since sorting still demands
that higher is better."""
if rtype != 'swiss':
return -1
for item in record.description.split():
item = item.split('=')
try:
if item[0] == 'PE' and len(item) == 2:
return 5 - int(item[1])
except IndexError:
continue
return -1
<｜fim▁end｜> | if protein.endswith('_{}'.format(mod)):
return '_{}'.format(mod)
elif protein.endswith('{}'.format(mod)):
return mod
elif protein.startswith('{}_'.format(mod)):
return '{}_'.format(mod)
elif protein.startswith('{}'.format(mod)):
return mod |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by keeping only the last one.
"""
records = {acc: (rec, get_record_type(rec)) for acc, rec in
SeqIO.index(fastafn, 'fasta').items()}
proteins = ((x,) for x in records.keys())
sequences = ((acc, str(rec.seq)) for acc, (rec, rtype) in records.items())
desc = ((acc, get_description(rec, rtype)) for acc, (rec, rtype) in records.items() if rtype)
evid = ((acc, get_uniprot_evidence_level(rec, rtype)) for acc, (rec, rtype) in
records.items())
ensgs = [(get_ensg(rec), acc) for acc, (rec, rtype) in records.items()
if rtype == 'ensembl']
def sym_out():
symbols = ((get_symbol(rec, rtype, fastadelim, genefield), acc) for
acc, (rec, rtype) in records.items() if rtype)
othergene = ((get_other_gene(rec, fastadelim, genefield), acc) for acc, (rec, rtype) in records.items()
if not rtype and fastadelim and fastadelim in rec.description)
yield from symbols
yield from othergene
return proteins, sequences, desc, evid, ensgs, [x for x in sym_out()]
def parse_fasta(fn):
with open(fn) as fp:
for record in SeqIO.parse(fp, 'fasta'):
yield record
def get_record_type(record):
dmod = get_decoy_mod_string(record.id)
test_name = record.id
if dmod is not None:
test_name = record.id.replace(dmod, '')
if test_name.split('|')[0] in ['sp', 'tr']:
return 'swiss'
elif test_name[:3] == 'ENS':
return 'ensembl'
else:
return False
def get_decoy_mod_string(protein):
mods = ['tryp_reverse', 'reverse', 'decoy', 'random', 'shuffle']
for mod in mods:
if mod in protein:
if protein.endswith('_{}'.format(mod)):
<|fim_middle|>
elif protein.endswith('{}'.format(mod)):
return mod
elif protein.startswith('{}_'.format(mod)):
return '{}_'.format(mod)
elif protein.startswith('{}'.format(mod)):
return mod
def get_description(record, rectype):
if rectype == 'ensembl':
desc_spl = [x.split(':') for x in record.description.split()]
try:
descix = [ix for ix, x in enumerate(desc_spl) if x[0] == 'description'][0]
except IndexError:
return 'NA'
desc = ' '.join([':'.join(x) for x in desc_spl[descix:]])[12:]
return desc
elif rectype == 'swiss':
desc = []
for part in record.description.split()[1:]:
if len(part.split('=')) > 1:
break
desc.append(part)
return ' '.join(desc)
def get_other_gene(record, fastadelim, genefield):
return record.description.split(fastadelim)[genefield]
def get_genes_pickfdr(fastafn, outputtype, fastadelim, genefield):
"""Called by protein FDR module for both ENSG and e.g. Uniprot"""
for rec in parse_fasta(fastafn):
rtype = get_record_type(rec)
if rtype == 'ensembl' and outputtype == 'ensg':
yield get_ensg(rec)
elif outputtype == 'genename':
yield get_symbol(rec, rtype, fastadelim, genefield)
def get_ensg(record):
fields = [x.split(':') for x in record.description.split()]
try:
return [x[1] for x in fields if x[0] == 'gene' and len(x) == 2][0]
except IndexError:
raise RuntimeError('ENSEMBL detected but cannot find gene ENSG in fasta')
def get_symbol(record, rectype, fastadelim, genefield):
if rectype == 'ensembl':
fields = [x.split(':') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'gene_symbol' and len(x) == 2]
elif rectype == 'swiss':
fields = [x.split('=') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'GN' and len(x) == 2]
elif fastadelim and fastadelim in record.description and genefield:
return record.description.split(fastadelim)[genefield]
else:
return 'NA'
try:
return sym[0]
except IndexError:
return 'NA'
def get_uniprot_evidence_level(record, rtype):
"""Returns uniprot protein existence evidence level for a fasta header.
Evidence levels are 1-5, but we return 5 - x since sorting still demands
that higher is better."""
if rtype != 'swiss':
return -1
for item in record.description.split():
item = item.split('=')
try:
if item[0] == 'PE' and len(item) == 2:
return 5 - int(item[1])
except IndexError:
continue
return -1
<｜fim▁end｜> | return '_{}'.format(mod) |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by keeping only the last one.
"""
records = {acc: (rec, get_record_type(rec)) for acc, rec in
SeqIO.index(fastafn, 'fasta').items()}
proteins = ((x,) for x in records.keys())
sequences = ((acc, str(rec.seq)) for acc, (rec, rtype) in records.items())
desc = ((acc, get_description(rec, rtype)) for acc, (rec, rtype) in records.items() if rtype)
evid = ((acc, get_uniprot_evidence_level(rec, rtype)) for acc, (rec, rtype) in
records.items())
ensgs = [(get_ensg(rec), acc) for acc, (rec, rtype) in records.items()
if rtype == 'ensembl']
def sym_out():
symbols = ((get_symbol(rec, rtype, fastadelim, genefield), acc) for
acc, (rec, rtype) in records.items() if rtype)
othergene = ((get_other_gene(rec, fastadelim, genefield), acc) for acc, (rec, rtype) in records.items()
if not rtype and fastadelim and fastadelim in rec.description)
yield from symbols
yield from othergene
return proteins, sequences, desc, evid, ensgs, [x for x in sym_out()]
def parse_fasta(fn):
with open(fn) as fp:
for record in SeqIO.parse(fp, 'fasta'):
yield record
def get_record_type(record):
dmod = get_decoy_mod_string(record.id)
test_name = record.id
if dmod is not None:
test_name = record.id.replace(dmod, '')
if test_name.split('|')[0] in ['sp', 'tr']:
return 'swiss'
elif test_name[:3] == 'ENS':
return 'ensembl'
else:
return False
def get_decoy_mod_string(protein):
mods = ['tryp_reverse', 'reverse', 'decoy', 'random', 'shuffle']
for mod in mods:
if mod in protein:
if protein.endswith('_{}'.format(mod)):
return '_{}'.format(mod)
elif protein.endswith('{}'.format(mod)):
<|fim_middle|>
elif protein.startswith('{}_'.format(mod)):
return '{}_'.format(mod)
elif protein.startswith('{}'.format(mod)):
return mod
def get_description(record, rectype):
if rectype == 'ensembl':
desc_spl = [x.split(':') for x in record.description.split()]
try:
descix = [ix for ix, x in enumerate(desc_spl) if x[0] == 'description'][0]
except IndexError:
return 'NA'
desc = ' '.join([':'.join(x) for x in desc_spl[descix:]])[12:]
return desc
elif rectype == 'swiss':
desc = []
for part in record.description.split()[1:]:
if len(part.split('=')) > 1:
break
desc.append(part)
return ' '.join(desc)
def get_other_gene(record, fastadelim, genefield):
return record.description.split(fastadelim)[genefield]
def get_genes_pickfdr(fastafn, outputtype, fastadelim, genefield):
"""Called by protein FDR module for both ENSG and e.g. Uniprot"""
for rec in parse_fasta(fastafn):
rtype = get_record_type(rec)
if rtype == 'ensembl' and outputtype == 'ensg':
yield get_ensg(rec)
elif outputtype == 'genename':
yield get_symbol(rec, rtype, fastadelim, genefield)
def get_ensg(record):
fields = [x.split(':') for x in record.description.split()]
try:
return [x[1] for x in fields if x[0] == 'gene' and len(x) == 2][0]
except IndexError:
raise RuntimeError('ENSEMBL detected but cannot find gene ENSG in fasta')
def get_symbol(record, rectype, fastadelim, genefield):
if rectype == 'ensembl':
fields = [x.split(':') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'gene_symbol' and len(x) == 2]
elif rectype == 'swiss':
fields = [x.split('=') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'GN' and len(x) == 2]
elif fastadelim and fastadelim in record.description and genefield:
return record.description.split(fastadelim)[genefield]
else:
return 'NA'
try:
return sym[0]
except IndexError:
return 'NA'
def get_uniprot_evidence_level(record, rtype):
"""Returns uniprot protein existence evidence level for a fasta header.
Evidence levels are 1-5, but we return 5 - x since sorting still demands
that higher is better."""
if rtype != 'swiss':
return -1
for item in record.description.split():
item = item.split('=')
try:
if item[0] == 'PE' and len(item) == 2:
return 5 - int(item[1])
except IndexError:
continue
return -1
<｜fim▁end｜> | return mod |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by keeping only the last one.
"""
records = {acc: (rec, get_record_type(rec)) for acc, rec in
SeqIO.index(fastafn, 'fasta').items()}
proteins = ((x,) for x in records.keys())
sequences = ((acc, str(rec.seq)) for acc, (rec, rtype) in records.items())
desc = ((acc, get_description(rec, rtype)) for acc, (rec, rtype) in records.items() if rtype)
evid = ((acc, get_uniprot_evidence_level(rec, rtype)) for acc, (rec, rtype) in
records.items())
ensgs = [(get_ensg(rec), acc) for acc, (rec, rtype) in records.items()
if rtype == 'ensembl']
def sym_out():
symbols = ((get_symbol(rec, rtype, fastadelim, genefield), acc) for
acc, (rec, rtype) in records.items() if rtype)
othergene = ((get_other_gene(rec, fastadelim, genefield), acc) for acc, (rec, rtype) in records.items()
if not rtype and fastadelim and fastadelim in rec.description)
yield from symbols
yield from othergene
return proteins, sequences, desc, evid, ensgs, [x for x in sym_out()]
def parse_fasta(fn):
with open(fn) as fp:
for record in SeqIO.parse(fp, 'fasta'):
yield record
def get_record_type(record):
dmod = get_decoy_mod_string(record.id)
test_name = record.id
if dmod is not None:
test_name = record.id.replace(dmod, '')
if test_name.split('|')[0] in ['sp', 'tr']:
return 'swiss'
elif test_name[:3] == 'ENS':
return 'ensembl'
else:
return False
def get_decoy_mod_string(protein):
mods = ['tryp_reverse', 'reverse', 'decoy', 'random', 'shuffle']
for mod in mods:
if mod in protein:
if protein.endswith('_{}'.format(mod)):
return '_{}'.format(mod)
elif protein.endswith('{}'.format(mod)):
return mod
elif protein.startswith('{}_'.format(mod)):
<|fim_middle|>
elif protein.startswith('{}'.format(mod)):
return mod
def get_description(record, rectype):
if rectype == 'ensembl':
desc_spl = [x.split(':') for x in record.description.split()]
try:
descix = [ix for ix, x in enumerate(desc_spl) if x[0] == 'description'][0]
except IndexError:
return 'NA'
desc = ' '.join([':'.join(x) for x in desc_spl[descix:]])[12:]
return desc
elif rectype == 'swiss':
desc = []
for part in record.description.split()[1:]:
if len(part.split('=')) > 1:
break
desc.append(part)
return ' '.join(desc)
def get_other_gene(record, fastadelim, genefield):
return record.description.split(fastadelim)[genefield]
def get_genes_pickfdr(fastafn, outputtype, fastadelim, genefield):
"""Called by protein FDR module for both ENSG and e.g. Uniprot"""
for rec in parse_fasta(fastafn):
rtype = get_record_type(rec)
if rtype == 'ensembl' and outputtype == 'ensg':
yield get_ensg(rec)
elif outputtype == 'genename':
yield get_symbol(rec, rtype, fastadelim, genefield)
def get_ensg(record):
fields = [x.split(':') for x in record.description.split()]
try:
return [x[1] for x in fields if x[0] == 'gene' and len(x) == 2][0]
except IndexError:
raise RuntimeError('ENSEMBL detected but cannot find gene ENSG in fasta')
def get_symbol(record, rectype, fastadelim, genefield):
if rectype == 'ensembl':
fields = [x.split(':') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'gene_symbol' and len(x) == 2]
elif rectype == 'swiss':
fields = [x.split('=') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'GN' and len(x) == 2]
elif fastadelim and fastadelim in record.description and genefield:
return record.description.split(fastadelim)[genefield]
else:
return 'NA'
try:
return sym[0]
except IndexError:
return 'NA'
def get_uniprot_evidence_level(record, rtype):
"""Returns uniprot protein existence evidence level for a fasta header.
Evidence levels are 1-5, but we return 5 - x since sorting still demands
that higher is better."""
if rtype != 'swiss':
return -1
for item in record.description.split():
item = item.split('=')
try:
if item[0] == 'PE' and len(item) == 2:
return 5 - int(item[1])
except IndexError:
continue
return -1
<｜fim▁end｜> | return '{}_'.format(mod) |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by keeping only the last one.
"""
records = {acc: (rec, get_record_type(rec)) for acc, rec in
SeqIO.index(fastafn, 'fasta').items()}
proteins = ((x,) for x in records.keys())
sequences = ((acc, str(rec.seq)) for acc, (rec, rtype) in records.items())
desc = ((acc, get_description(rec, rtype)) for acc, (rec, rtype) in records.items() if rtype)
evid = ((acc, get_uniprot_evidence_level(rec, rtype)) for acc, (rec, rtype) in
records.items())
ensgs = [(get_ensg(rec), acc) for acc, (rec, rtype) in records.items()
if rtype == 'ensembl']
def sym_out():
symbols = ((get_symbol(rec, rtype, fastadelim, genefield), acc) for
acc, (rec, rtype) in records.items() if rtype)
othergene = ((get_other_gene(rec, fastadelim, genefield), acc) for acc, (rec, rtype) in records.items()
if not rtype and fastadelim and fastadelim in rec.description)
yield from symbols
yield from othergene
return proteins, sequences, desc, evid, ensgs, [x for x in sym_out()]
def parse_fasta(fn):
with open(fn) as fp:
for record in SeqIO.parse(fp, 'fasta'):
yield record
def get_record_type(record):
dmod = get_decoy_mod_string(record.id)
test_name = record.id
if dmod is not None:
test_name = record.id.replace(dmod, '')
if test_name.split('|')[0] in ['sp', 'tr']:
return 'swiss'
elif test_name[:3] == 'ENS':
return 'ensembl'
else:
return False
def get_decoy_mod_string(protein):
mods = ['tryp_reverse', 'reverse', 'decoy', 'random', 'shuffle']
for mod in mods:
if mod in protein:
if protein.endswith('_{}'.format(mod)):
return '_{}'.format(mod)
elif protein.endswith('{}'.format(mod)):
return mod
elif protein.startswith('{}_'.format(mod)):
return '{}_'.format(mod)
elif protein.startswith('{}'.format(mod)):
<|fim_middle|>
def get_description(record, rectype):
if rectype == 'ensembl':
desc_spl = [x.split(':') for x in record.description.split()]
try:
descix = [ix for ix, x in enumerate(desc_spl) if x[0] == 'description'][0]
except IndexError:
return 'NA'
desc = ' '.join([':'.join(x) for x in desc_spl[descix:]])[12:]
return desc
elif rectype == 'swiss':
desc = []
for part in record.description.split()[1:]:
if len(part.split('=')) > 1:
break
desc.append(part)
return ' '.join(desc)
def get_other_gene(record, fastadelim, genefield):
return record.description.split(fastadelim)[genefield]
def get_genes_pickfdr(fastafn, outputtype, fastadelim, genefield):
"""Called by protein FDR module for both ENSG and e.g. Uniprot"""
for rec in parse_fasta(fastafn):
rtype = get_record_type(rec)
if rtype == 'ensembl' and outputtype == 'ensg':
yield get_ensg(rec)
elif outputtype == 'genename':
yield get_symbol(rec, rtype, fastadelim, genefield)
def get_ensg(record):
fields = [x.split(':') for x in record.description.split()]
try:
return [x[1] for x in fields if x[0] == 'gene' and len(x) == 2][0]
except IndexError:
raise RuntimeError('ENSEMBL detected but cannot find gene ENSG in fasta')
def get_symbol(record, rectype, fastadelim, genefield):
if rectype == 'ensembl':
fields = [x.split(':') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'gene_symbol' and len(x) == 2]
elif rectype == 'swiss':
fields = [x.split('=') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'GN' and len(x) == 2]
elif fastadelim and fastadelim in record.description and genefield:
return record.description.split(fastadelim)[genefield]
else:
return 'NA'
try:
return sym[0]
except IndexError:
return 'NA'
def get_uniprot_evidence_level(record, rtype):
"""Returns uniprot protein existence evidence level for a fasta header.
Evidence levels are 1-5, but we return 5 - x since sorting still demands
that higher is better."""
if rtype != 'swiss':
return -1
for item in record.description.split():
item = item.split('=')
try:
if item[0] == 'PE' and len(item) == 2:
return 5 - int(item[1])
except IndexError:
continue
return -1
<｜fim▁end｜> | return mod |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by keeping only the last one.
"""
records = {acc: (rec, get_record_type(rec)) for acc, rec in
SeqIO.index(fastafn, 'fasta').items()}
proteins = ((x,) for x in records.keys())
sequences = ((acc, str(rec.seq)) for acc, (rec, rtype) in records.items())
desc = ((acc, get_description(rec, rtype)) for acc, (rec, rtype) in records.items() if rtype)
evid = ((acc, get_uniprot_evidence_level(rec, rtype)) for acc, (rec, rtype) in
records.items())
ensgs = [(get_ensg(rec), acc) for acc, (rec, rtype) in records.items()
if rtype == 'ensembl']
def sym_out():
symbols = ((get_symbol(rec, rtype, fastadelim, genefield), acc) for
acc, (rec, rtype) in records.items() if rtype)
othergene = ((get_other_gene(rec, fastadelim, genefield), acc) for acc, (rec, rtype) in records.items()
if not rtype and fastadelim and fastadelim in rec.description)
yield from symbols
yield from othergene
return proteins, sequences, desc, evid, ensgs, [x for x in sym_out()]
def parse_fasta(fn):
with open(fn) as fp:
for record in SeqIO.parse(fp, 'fasta'):
yield record
def get_record_type(record):
dmod = get_decoy_mod_string(record.id)
test_name = record.id
if dmod is not None:
test_name = record.id.replace(dmod, '')
if test_name.split('|')[0] in ['sp', 'tr']:
return 'swiss'
elif test_name[:3] == 'ENS':
return 'ensembl'
else:
return False
def get_decoy_mod_string(protein):
mods = ['tryp_reverse', 'reverse', 'decoy', 'random', 'shuffle']
for mod in mods:
if mod in protein:
if protein.endswith('_{}'.format(mod)):
return '_{}'.format(mod)
elif protein.endswith('{}'.format(mod)):
return mod
elif protein.startswith('{}_'.format(mod)):
return '{}_'.format(mod)
elif protein.startswith('{}'.format(mod)):
return mod
def get_description(record, rectype):
if rectype == 'ensembl':
<|fim_middle|>
elif rectype == 'swiss':
desc = []
for part in record.description.split()[1:]:
if len(part.split('=')) > 1:
break
desc.append(part)
return ' '.join(desc)
def get_other_gene(record, fastadelim, genefield):
return record.description.split(fastadelim)[genefield]
def get_genes_pickfdr(fastafn, outputtype, fastadelim, genefield):
"""Called by protein FDR module for both ENSG and e.g. Uniprot"""
for rec in parse_fasta(fastafn):
rtype = get_record_type(rec)
if rtype == 'ensembl' and outputtype == 'ensg':
yield get_ensg(rec)
elif outputtype == 'genename':
yield get_symbol(rec, rtype, fastadelim, genefield)
def get_ensg(record):
fields = [x.split(':') for x in record.description.split()]
try:
return [x[1] for x in fields if x[0] == 'gene' and len(x) == 2][0]
except IndexError:
raise RuntimeError('ENSEMBL detected but cannot find gene ENSG in fasta')
def get_symbol(record, rectype, fastadelim, genefield):
if rectype == 'ensembl':
fields = [x.split(':') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'gene_symbol' and len(x) == 2]
elif rectype == 'swiss':
fields = [x.split('=') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'GN' and len(x) == 2]
elif fastadelim and fastadelim in record.description and genefield:
return record.description.split(fastadelim)[genefield]
else:
return 'NA'
try:
return sym[0]
except IndexError:
return 'NA'
def get_uniprot_evidence_level(record, rtype):
"""Returns uniprot protein existence evidence level for a fasta header.
Evidence levels are 1-5, but we return 5 - x since sorting still demands
that higher is better."""
if rtype != 'swiss':
return -1
for item in record.description.split():
item = item.split('=')
try:
if item[0] == 'PE' and len(item) == 2:
return 5 - int(item[1])
except IndexError:
continue
return -1
<｜fim▁end｜> | desc_spl = [x.split(':') for x in record.description.split()]
try:
descix = [ix for ix, x in enumerate(desc_spl) if x[0] == 'description'][0]
except IndexError:
return 'NA'
desc = ' '.join([':'.join(x) for x in desc_spl[descix:]])[12:]
return desc |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by keeping only the last one.
"""
records = {acc: (rec, get_record_type(rec)) for acc, rec in
SeqIO.index(fastafn, 'fasta').items()}
proteins = ((x,) for x in records.keys())
sequences = ((acc, str(rec.seq)) for acc, (rec, rtype) in records.items())
desc = ((acc, get_description(rec, rtype)) for acc, (rec, rtype) in records.items() if rtype)
evid = ((acc, get_uniprot_evidence_level(rec, rtype)) for acc, (rec, rtype) in
records.items())
ensgs = [(get_ensg(rec), acc) for acc, (rec, rtype) in records.items()
if rtype == 'ensembl']
def sym_out():
symbols = ((get_symbol(rec, rtype, fastadelim, genefield), acc) for
acc, (rec, rtype) in records.items() if rtype)
othergene = ((get_other_gene(rec, fastadelim, genefield), acc) for acc, (rec, rtype) in records.items()
if not rtype and fastadelim and fastadelim in rec.description)
yield from symbols
yield from othergene
return proteins, sequences, desc, evid, ensgs, [x for x in sym_out()]
def parse_fasta(fn):
with open(fn) as fp:
for record in SeqIO.parse(fp, 'fasta'):
yield record
def get_record_type(record):
dmod = get_decoy_mod_string(record.id)
test_name = record.id
if dmod is not None:
test_name = record.id.replace(dmod, '')
if test_name.split('|')[0] in ['sp', 'tr']:
return 'swiss'
elif test_name[:3] == 'ENS':
return 'ensembl'
else:
return False
def get_decoy_mod_string(protein):
mods = ['tryp_reverse', 'reverse', 'decoy', 'random', 'shuffle']
for mod in mods:
if mod in protein:
if protein.endswith('_{}'.format(mod)):
return '_{}'.format(mod)
elif protein.endswith('{}'.format(mod)):
return mod
elif protein.startswith('{}_'.format(mod)):
return '{}_'.format(mod)
elif protein.startswith('{}'.format(mod)):
return mod
def get_description(record, rectype):
if rectype == 'ensembl':
desc_spl = [x.split(':') for x in record.description.split()]
try:
descix = [ix for ix, x in enumerate(desc_spl) if x[0] == 'description'][0]
except IndexError:
return 'NA'
desc = ' '.join([':'.join(x) for x in desc_spl[descix:]])[12:]
return desc
elif rectype == 'swiss':
<|fim_middle|>
def get_other_gene(record, fastadelim, genefield):
return record.description.split(fastadelim)[genefield]
def get_genes_pickfdr(fastafn, outputtype, fastadelim, genefield):
"""Called by protein FDR module for both ENSG and e.g. Uniprot"""
for rec in parse_fasta(fastafn):
rtype = get_record_type(rec)
if rtype == 'ensembl' and outputtype == 'ensg':
yield get_ensg(rec)
elif outputtype == 'genename':
yield get_symbol(rec, rtype, fastadelim, genefield)
def get_ensg(record):
fields = [x.split(':') for x in record.description.split()]
try:
return [x[1] for x in fields if x[0] == 'gene' and len(x) == 2][0]
except IndexError:
raise RuntimeError('ENSEMBL detected but cannot find gene ENSG in fasta')
def get_symbol(record, rectype, fastadelim, genefield):
if rectype == 'ensembl':
fields = [x.split(':') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'gene_symbol' and len(x) == 2]
elif rectype == 'swiss':
fields = [x.split('=') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'GN' and len(x) == 2]
elif fastadelim and fastadelim in record.description and genefield:
return record.description.split(fastadelim)[genefield]
else:
return 'NA'
try:
return sym[0]
except IndexError:
return 'NA'
def get_uniprot_evidence_level(record, rtype):
"""Returns uniprot protein existence evidence level for a fasta header.
Evidence levels are 1-5, but we return 5 - x since sorting still demands
that higher is better."""
if rtype != 'swiss':
return -1
for item in record.description.split():
item = item.split('=')
try:
if item[0] == 'PE' and len(item) == 2:
return 5 - int(item[1])
except IndexError:
continue
return -1
<｜fim▁end｜> | desc = []
for part in record.description.split()[1:]:
if len(part.split('=')) > 1:
break
desc.append(part)
return ' '.join(desc) |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by keeping only the last one.
"""
records = {acc: (rec, get_record_type(rec)) for acc, rec in
SeqIO.index(fastafn, 'fasta').items()}
proteins = ((x,) for x in records.keys())
sequences = ((acc, str(rec.seq)) for acc, (rec, rtype) in records.items())
desc = ((acc, get_description(rec, rtype)) for acc, (rec, rtype) in records.items() if rtype)
evid = ((acc, get_uniprot_evidence_level(rec, rtype)) for acc, (rec, rtype) in
records.items())
ensgs = [(get_ensg(rec), acc) for acc, (rec, rtype) in records.items()
if rtype == 'ensembl']
def sym_out():
symbols = ((get_symbol(rec, rtype, fastadelim, genefield), acc) for
acc, (rec, rtype) in records.items() if rtype)
othergene = ((get_other_gene(rec, fastadelim, genefield), acc) for acc, (rec, rtype) in records.items()
if not rtype and fastadelim and fastadelim in rec.description)
yield from symbols
yield from othergene
return proteins, sequences, desc, evid, ensgs, [x for x in sym_out()]
def parse_fasta(fn):
with open(fn) as fp:
for record in SeqIO.parse(fp, 'fasta'):
yield record
def get_record_type(record):
dmod = get_decoy_mod_string(record.id)
test_name = record.id
if dmod is not None:
test_name = record.id.replace(dmod, '')
if test_name.split('|')[0] in ['sp', 'tr']:
return 'swiss'
elif test_name[:3] == 'ENS':
return 'ensembl'
else:
return False
def get_decoy_mod_string(protein):
mods = ['tryp_reverse', 'reverse', 'decoy', 'random', 'shuffle']
for mod in mods:
if mod in protein:
if protein.endswith('_{}'.format(mod)):
return '_{}'.format(mod)
elif protein.endswith('{}'.format(mod)):
return mod
elif protein.startswith('{}_'.format(mod)):
return '{}_'.format(mod)
elif protein.startswith('{}'.format(mod)):
return mod
def get_description(record, rectype):
if rectype == 'ensembl':
desc_spl = [x.split(':') for x in record.description.split()]
try:
descix = [ix for ix, x in enumerate(desc_spl) if x[0] == 'description'][0]
except IndexError:
return 'NA'
desc = ' '.join([':'.join(x) for x in desc_spl[descix:]])[12:]
return desc
elif rectype == 'swiss':
desc = []
for part in record.description.split()[1:]:
if len(part.split('=')) > 1:
<|fim_middle|>
desc.append(part)
return ' '.join(desc)
def get_other_gene(record, fastadelim, genefield):
return record.description.split(fastadelim)[genefield]
def get_genes_pickfdr(fastafn, outputtype, fastadelim, genefield):
"""Called by protein FDR module for both ENSG and e.g. Uniprot"""
for rec in parse_fasta(fastafn):
rtype = get_record_type(rec)
if rtype == 'ensembl' and outputtype == 'ensg':
yield get_ensg(rec)
elif outputtype == 'genename':
yield get_symbol(rec, rtype, fastadelim, genefield)
def get_ensg(record):
fields = [x.split(':') for x in record.description.split()]
try:
return [x[1] for x in fields if x[0] == 'gene' and len(x) == 2][0]
except IndexError:
raise RuntimeError('ENSEMBL detected but cannot find gene ENSG in fasta')
def get_symbol(record, rectype, fastadelim, genefield):
if rectype == 'ensembl':
fields = [x.split(':') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'gene_symbol' and len(x) == 2]
elif rectype == 'swiss':
fields = [x.split('=') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'GN' and len(x) == 2]
elif fastadelim and fastadelim in record.description and genefield:
return record.description.split(fastadelim)[genefield]
else:
return 'NA'
try:
return sym[0]
except IndexError:
return 'NA'
def get_uniprot_evidence_level(record, rtype):
"""Returns uniprot protein existence evidence level for a fasta header.
Evidence levels are 1-5, but we return 5 - x since sorting still demands
that higher is better."""
if rtype != 'swiss':
return -1
for item in record.description.split():
item = item.split('=')
try:
if item[0] == 'PE' and len(item) == 2:
return 5 - int(item[1])
except IndexError:
continue
return -1
<｜fim▁end｜> | break |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by keeping only the last one.
"""
records = {acc: (rec, get_record_type(rec)) for acc, rec in
SeqIO.index(fastafn, 'fasta').items()}
proteins = ((x,) for x in records.keys())
sequences = ((acc, str(rec.seq)) for acc, (rec, rtype) in records.items())
desc = ((acc, get_description(rec, rtype)) for acc, (rec, rtype) in records.items() if rtype)
evid = ((acc, get_uniprot_evidence_level(rec, rtype)) for acc, (rec, rtype) in
records.items())
ensgs = [(get_ensg(rec), acc) for acc, (rec, rtype) in records.items()
if rtype == 'ensembl']
def sym_out():
symbols = ((get_symbol(rec, rtype, fastadelim, genefield), acc) for
acc, (rec, rtype) in records.items() if rtype)
othergene = ((get_other_gene(rec, fastadelim, genefield), acc) for acc, (rec, rtype) in records.items()
if not rtype and fastadelim and fastadelim in rec.description)
yield from symbols
yield from othergene
return proteins, sequences, desc, evid, ensgs, [x for x in sym_out()]
def parse_fasta(fn):
with open(fn) as fp:
for record in SeqIO.parse(fp, 'fasta'):
yield record
def get_record_type(record):
dmod = get_decoy_mod_string(record.id)
test_name = record.id
if dmod is not None:
test_name = record.id.replace(dmod, '')
if test_name.split('|')[0] in ['sp', 'tr']:
return 'swiss'
elif test_name[:3] == 'ENS':
return 'ensembl'
else:
return False
def get_decoy_mod_string(protein):
mods = ['tryp_reverse', 'reverse', 'decoy', 'random', 'shuffle']
for mod in mods:
if mod in protein:
if protein.endswith('_{}'.format(mod)):
return '_{}'.format(mod)
elif protein.endswith('{}'.format(mod)):
return mod
elif protein.startswith('{}_'.format(mod)):
return '{}_'.format(mod)
elif protein.startswith('{}'.format(mod)):
return mod
def get_description(record, rectype):
if rectype == 'ensembl':
desc_spl = [x.split(':') for x in record.description.split()]
try:
descix = [ix for ix, x in enumerate(desc_spl) if x[0] == 'description'][0]
except IndexError:
return 'NA'
desc = ' '.join([':'.join(x) for x in desc_spl[descix:]])[12:]
return desc
elif rectype == 'swiss':
desc = []
for part in record.description.split()[1:]:
if len(part.split('=')) > 1:
break
desc.append(part)
return ' '.join(desc)
def get_other_gene(record, fastadelim, genefield):
return record.description.split(fastadelim)[genefield]
def get_genes_pickfdr(fastafn, outputtype, fastadelim, genefield):
"""Called by protein FDR module for both ENSG and e.g. Uniprot"""
for rec in parse_fasta(fastafn):
rtype = get_record_type(rec)
if rtype == 'ensembl' and outputtype == 'ensg':
<|fim_middle|>
elif outputtype == 'genename':
yield get_symbol(rec, rtype, fastadelim, genefield)
def get_ensg(record):
fields = [x.split(':') for x in record.description.split()]
try:
return [x[1] for x in fields if x[0] == 'gene' and len(x) == 2][0]
except IndexError:
raise RuntimeError('ENSEMBL detected but cannot find gene ENSG in fasta')
def get_symbol(record, rectype, fastadelim, genefield):
if rectype == 'ensembl':
fields = [x.split(':') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'gene_symbol' and len(x) == 2]
elif rectype == 'swiss':
fields = [x.split('=') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'GN' and len(x) == 2]
elif fastadelim and fastadelim in record.description and genefield:
return record.description.split(fastadelim)[genefield]
else:
return 'NA'
try:
return sym[0]
except IndexError:
return 'NA'
def get_uniprot_evidence_level(record, rtype):
"""Returns uniprot protein existence evidence level for a fasta header.
Evidence levels are 1-5, but we return 5 - x since sorting still demands
that higher is better."""
if rtype != 'swiss':
return -1
for item in record.description.split():
item = item.split('=')
try:
if item[0] == 'PE' and len(item) == 2:
return 5 - int(item[1])
except IndexError:
continue
return -1
<｜fim▁end｜> | yield get_ensg(rec) |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by keeping only the last one.
"""
records = {acc: (rec, get_record_type(rec)) for acc, rec in
SeqIO.index(fastafn, 'fasta').items()}
proteins = ((x,) for x in records.keys())
sequences = ((acc, str(rec.seq)) for acc, (rec, rtype) in records.items())
desc = ((acc, get_description(rec, rtype)) for acc, (rec, rtype) in records.items() if rtype)
evid = ((acc, get_uniprot_evidence_level(rec, rtype)) for acc, (rec, rtype) in
records.items())
ensgs = [(get_ensg(rec), acc) for acc, (rec, rtype) in records.items()
if rtype == 'ensembl']
def sym_out():
symbols = ((get_symbol(rec, rtype, fastadelim, genefield), acc) for
acc, (rec, rtype) in records.items() if rtype)
othergene = ((get_other_gene(rec, fastadelim, genefield), acc) for acc, (rec, rtype) in records.items()
if not rtype and fastadelim and fastadelim in rec.description)
yield from symbols
yield from othergene
return proteins, sequences, desc, evid, ensgs, [x for x in sym_out()]
def parse_fasta(fn):
with open(fn) as fp:
for record in SeqIO.parse(fp, 'fasta'):
yield record
def get_record_type(record):
dmod = get_decoy_mod_string(record.id)
test_name = record.id
if dmod is not None:
test_name = record.id.replace(dmod, '')
if test_name.split('|')[0] in ['sp', 'tr']:
return 'swiss'
elif test_name[:3] == 'ENS':
return 'ensembl'
else:
return False
def get_decoy_mod_string(protein):
mods = ['tryp_reverse', 'reverse', 'decoy', 'random', 'shuffle']
for mod in mods:
if mod in protein:
if protein.endswith('_{}'.format(mod)):
return '_{}'.format(mod)
elif protein.endswith('{}'.format(mod)):
return mod
elif protein.startswith('{}_'.format(mod)):
return '{}_'.format(mod)
elif protein.startswith('{}'.format(mod)):
return mod
def get_description(record, rectype):
if rectype == 'ensembl':
desc_spl = [x.split(':') for x in record.description.split()]
try:
descix = [ix for ix, x in enumerate(desc_spl) if x[0] == 'description'][0]
except IndexError:
return 'NA'
desc = ' '.join([':'.join(x) for x in desc_spl[descix:]])[12:]
return desc
elif rectype == 'swiss':
desc = []
for part in record.description.split()[1:]:
if len(part.split('=')) > 1:
break
desc.append(part)
return ' '.join(desc)
def get_other_gene(record, fastadelim, genefield):
return record.description.split(fastadelim)[genefield]
def get_genes_pickfdr(fastafn, outputtype, fastadelim, genefield):
"""Called by protein FDR module for both ENSG and e.g. Uniprot"""
for rec in parse_fasta(fastafn):
rtype = get_record_type(rec)
if rtype == 'ensembl' and outputtype == 'ensg':
yield get_ensg(rec)
elif outputtype == 'genename':
<|fim_middle|>
def get_ensg(record):
fields = [x.split(':') for x in record.description.split()]
try:
return [x[1] for x in fields if x[0] == 'gene' and len(x) == 2][0]
except IndexError:
raise RuntimeError('ENSEMBL detected but cannot find gene ENSG in fasta')
def get_symbol(record, rectype, fastadelim, genefield):
if rectype == 'ensembl':
fields = [x.split(':') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'gene_symbol' and len(x) == 2]
elif rectype == 'swiss':
fields = [x.split('=') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'GN' and len(x) == 2]
elif fastadelim and fastadelim in record.description and genefield:
return record.description.split(fastadelim)[genefield]
else:
return 'NA'
try:
return sym[0]
except IndexError:
return 'NA'
def get_uniprot_evidence_level(record, rtype):
"""Returns uniprot protein existence evidence level for a fasta header.
Evidence levels are 1-5, but we return 5 - x since sorting still demands
that higher is better."""
if rtype != 'swiss':
return -1
for item in record.description.split():
item = item.split('=')
try:
if item[0] == 'PE' and len(item) == 2:
return 5 - int(item[1])
except IndexError:
continue
return -1
<｜fim▁end｜> | yield get_symbol(rec, rtype, fastadelim, genefield) |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by keeping only the last one.
"""
records = {acc: (rec, get_record_type(rec)) for acc, rec in
SeqIO.index(fastafn, 'fasta').items()}
proteins = ((x,) for x in records.keys())
sequences = ((acc, str(rec.seq)) for acc, (rec, rtype) in records.items())
desc = ((acc, get_description(rec, rtype)) for acc, (rec, rtype) in records.items() if rtype)
evid = ((acc, get_uniprot_evidence_level(rec, rtype)) for acc, (rec, rtype) in
records.items())
ensgs = [(get_ensg(rec), acc) for acc, (rec, rtype) in records.items()
if rtype == 'ensembl']
def sym_out():
symbols = ((get_symbol(rec, rtype, fastadelim, genefield), acc) for
acc, (rec, rtype) in records.items() if rtype)
othergene = ((get_other_gene(rec, fastadelim, genefield), acc) for acc, (rec, rtype) in records.items()
if not rtype and fastadelim and fastadelim in rec.description)
yield from symbols
yield from othergene
return proteins, sequences, desc, evid, ensgs, [x for x in sym_out()]
def parse_fasta(fn):
with open(fn) as fp:
for record in SeqIO.parse(fp, 'fasta'):
yield record
def get_record_type(record):
dmod = get_decoy_mod_string(record.id)
test_name = record.id
if dmod is not None:
test_name = record.id.replace(dmod, '')
if test_name.split('|')[0] in ['sp', 'tr']:
return 'swiss'
elif test_name[:3] == 'ENS':
return 'ensembl'
else:
return False
def get_decoy_mod_string(protein):
mods = ['tryp_reverse', 'reverse', 'decoy', 'random', 'shuffle']
for mod in mods:
if mod in protein:
if protein.endswith('_{}'.format(mod)):
return '_{}'.format(mod)
elif protein.endswith('{}'.format(mod)):
return mod
elif protein.startswith('{}_'.format(mod)):
return '{}_'.format(mod)
elif protein.startswith('{}'.format(mod)):
return mod
def get_description(record, rectype):
if rectype == 'ensembl':
desc_spl = [x.split(':') for x in record.description.split()]
try:
descix = [ix for ix, x in enumerate(desc_spl) if x[0] == 'description'][0]
except IndexError:
return 'NA'
desc = ' '.join([':'.join(x) for x in desc_spl[descix:]])[12:]
return desc
elif rectype == 'swiss':
desc = []
for part in record.description.split()[1:]:
if len(part.split('=')) > 1:
break
desc.append(part)
return ' '.join(desc)
def get_other_gene(record, fastadelim, genefield):
return record.description.split(fastadelim)[genefield]
def get_genes_pickfdr(fastafn, outputtype, fastadelim, genefield):
"""Called by protein FDR module for both ENSG and e.g. Uniprot"""
for rec in parse_fasta(fastafn):
rtype = get_record_type(rec)
if rtype == 'ensembl' and outputtype == 'ensg':
yield get_ensg(rec)
elif outputtype == 'genename':
yield get_symbol(rec, rtype, fastadelim, genefield)
def get_ensg(record):
fields = [x.split(':') for x in record.description.split()]
try:
return [x[1] for x in fields if x[0] == 'gene' and len(x) == 2][0]
except IndexError:
raise RuntimeError('ENSEMBL detected but cannot find gene ENSG in fasta')
def get_symbol(record, rectype, fastadelim, genefield):
if rectype == 'ensembl':
<|fim_middle|>
elif rectype == 'swiss':
fields = [x.split('=') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'GN' and len(x) == 2]
elif fastadelim and fastadelim in record.description and genefield:
return record.description.split(fastadelim)[genefield]
else:
return 'NA'
try:
return sym[0]
except IndexError:
return 'NA'
def get_uniprot_evidence_level(record, rtype):
"""Returns uniprot protein existence evidence level for a fasta header.
Evidence levels are 1-5, but we return 5 - x since sorting still demands
that higher is better."""
if rtype != 'swiss':
return -1
for item in record.description.split():
item = item.split('=')
try:
if item[0] == 'PE' and len(item) == 2:
return 5 - int(item[1])
except IndexError:
continue
return -1
<｜fim▁end｜> | fields = [x.split(':') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'gene_symbol' and len(x) == 2] |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by keeping only the last one.
"""
records = {acc: (rec, get_record_type(rec)) for acc, rec in
SeqIO.index(fastafn, 'fasta').items()}
proteins = ((x,) for x in records.keys())
sequences = ((acc, str(rec.seq)) for acc, (rec, rtype) in records.items())
desc = ((acc, get_description(rec, rtype)) for acc, (rec, rtype) in records.items() if rtype)
evid = ((acc, get_uniprot_evidence_level(rec, rtype)) for acc, (rec, rtype) in
records.items())
ensgs = [(get_ensg(rec), acc) for acc, (rec, rtype) in records.items()
if rtype == 'ensembl']
def sym_out():
symbols = ((get_symbol(rec, rtype, fastadelim, genefield), acc) for
acc, (rec, rtype) in records.items() if rtype)
othergene = ((get_other_gene(rec, fastadelim, genefield), acc) for acc, (rec, rtype) in records.items()
if not rtype and fastadelim and fastadelim in rec.description)
yield from symbols
yield from othergene
return proteins, sequences, desc, evid, ensgs, [x for x in sym_out()]
def parse_fasta(fn):
with open(fn) as fp:
for record in SeqIO.parse(fp, 'fasta'):
yield record
def get_record_type(record):
dmod = get_decoy_mod_string(record.id)
test_name = record.id
if dmod is not None:
test_name = record.id.replace(dmod, '')
if test_name.split('|')[0] in ['sp', 'tr']:
return 'swiss'
elif test_name[:3] == 'ENS':
return 'ensembl'
else:
return False
def get_decoy_mod_string(protein):
mods = ['tryp_reverse', 'reverse', 'decoy', 'random', 'shuffle']
for mod in mods:
if mod in protein:
if protein.endswith('_{}'.format(mod)):
return '_{}'.format(mod)
elif protein.endswith('{}'.format(mod)):
return mod
elif protein.startswith('{}_'.format(mod)):
return '{}_'.format(mod)
elif protein.startswith('{}'.format(mod)):
return mod
def get_description(record, rectype):
if rectype == 'ensembl':
desc_spl = [x.split(':') for x in record.description.split()]
try:
descix = [ix for ix, x in enumerate(desc_spl) if x[0] == 'description'][0]
except IndexError:
return 'NA'
desc = ' '.join([':'.join(x) for x in desc_spl[descix:]])[12:]
return desc
elif rectype == 'swiss':
desc = []
for part in record.description.split()[1:]:
if len(part.split('=')) > 1:
break
desc.append(part)
return ' '.join(desc)
def get_other_gene(record, fastadelim, genefield):
return record.description.split(fastadelim)[genefield]
def get_genes_pickfdr(fastafn, outputtype, fastadelim, genefield):
"""Called by protein FDR module for both ENSG and e.g. Uniprot"""
for rec in parse_fasta(fastafn):
rtype = get_record_type(rec)
if rtype == 'ensembl' and outputtype == 'ensg':
yield get_ensg(rec)
elif outputtype == 'genename':
yield get_symbol(rec, rtype, fastadelim, genefield)
def get_ensg(record):
fields = [x.split(':') for x in record.description.split()]
try:
return [x[1] for x in fields if x[0] == 'gene' and len(x) == 2][0]
except IndexError:
raise RuntimeError('ENSEMBL detected but cannot find gene ENSG in fasta')
def get_symbol(record, rectype, fastadelim, genefield):
if rectype == 'ensembl':
fields = [x.split(':') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'gene_symbol' and len(x) == 2]
elif rectype == 'swiss':
<|fim_middle|>
elif fastadelim and fastadelim in record.description and genefield:
return record.description.split(fastadelim)[genefield]
else:
return 'NA'
try:
return sym[0]
except IndexError:
return 'NA'
def get_uniprot_evidence_level(record, rtype):
"""Returns uniprot protein existence evidence level for a fasta header.
Evidence levels are 1-5, but we return 5 - x since sorting still demands
that higher is better."""
if rtype != 'swiss':
return -1
for item in record.description.split():
item = item.split('=')
try:
if item[0] == 'PE' and len(item) == 2:
return 5 - int(item[1])
except IndexError:
continue
return -1
<｜fim▁end｜> | fields = [x.split('=') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'GN' and len(x) == 2] |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by keeping only the last one.
"""
records = {acc: (rec, get_record_type(rec)) for acc, rec in
SeqIO.index(fastafn, 'fasta').items()}
proteins = ((x,) for x in records.keys())
sequences = ((acc, str(rec.seq)) for acc, (rec, rtype) in records.items())
desc = ((acc, get_description(rec, rtype)) for acc, (rec, rtype) in records.items() if rtype)
evid = ((acc, get_uniprot_evidence_level(rec, rtype)) for acc, (rec, rtype) in
records.items())
ensgs = [(get_ensg(rec), acc) for acc, (rec, rtype) in records.items()
if rtype == 'ensembl']
def sym_out():
symbols = ((get_symbol(rec, rtype, fastadelim, genefield), acc) for
acc, (rec, rtype) in records.items() if rtype)
othergene = ((get_other_gene(rec, fastadelim, genefield), acc) for acc, (rec, rtype) in records.items()
if not rtype and fastadelim and fastadelim in rec.description)
yield from symbols
yield from othergene
return proteins, sequences, desc, evid, ensgs, [x for x in sym_out()]
def parse_fasta(fn):
with open(fn) as fp:
for record in SeqIO.parse(fp, 'fasta'):
yield record
def get_record_type(record):
dmod = get_decoy_mod_string(record.id)
test_name = record.id
if dmod is not None:
test_name = record.id.replace(dmod, '')
if test_name.split('|')[0] in ['sp', 'tr']:
return 'swiss'
elif test_name[:3] == 'ENS':
return 'ensembl'
else:
return False
def get_decoy_mod_string(protein):
mods = ['tryp_reverse', 'reverse', 'decoy', 'random', 'shuffle']
for mod in mods:
if mod in protein:
if protein.endswith('_{}'.format(mod)):
return '_{}'.format(mod)
elif protein.endswith('{}'.format(mod)):
return mod
elif protein.startswith('{}_'.format(mod)):
return '{}_'.format(mod)
elif protein.startswith('{}'.format(mod)):
return mod
def get_description(record, rectype):
if rectype == 'ensembl':
desc_spl = [x.split(':') for x in record.description.split()]
try:
descix = [ix for ix, x in enumerate(desc_spl) if x[0] == 'description'][0]
except IndexError:
return 'NA'
desc = ' '.join([':'.join(x) for x in desc_spl[descix:]])[12:]
return desc
elif rectype == 'swiss':
desc = []
for part in record.description.split()[1:]:
if len(part.split('=')) > 1:
break
desc.append(part)
return ' '.join(desc)
def get_other_gene(record, fastadelim, genefield):
return record.description.split(fastadelim)[genefield]
def get_genes_pickfdr(fastafn, outputtype, fastadelim, genefield):
"""Called by protein FDR module for both ENSG and e.g. Uniprot"""
for rec in parse_fasta(fastafn):
rtype = get_record_type(rec)
if rtype == 'ensembl' and outputtype == 'ensg':
yield get_ensg(rec)
elif outputtype == 'genename':
yield get_symbol(rec, rtype, fastadelim, genefield)
def get_ensg(record):
fields = [x.split(':') for x in record.description.split()]
try:
return [x[1] for x in fields if x[0] == 'gene' and len(x) == 2][0]
except IndexError:
raise RuntimeError('ENSEMBL detected but cannot find gene ENSG in fasta')
def get_symbol(record, rectype, fastadelim, genefield):
if rectype == 'ensembl':
fields = [x.split(':') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'gene_symbol' and len(x) == 2]
elif rectype == 'swiss':
fields = [x.split('=') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'GN' and len(x) == 2]
elif fastadelim and fastadelim in record.description and genefield:
<|fim_middle|>
else:
return 'NA'
try:
return sym[0]
except IndexError:
return 'NA'
def get_uniprot_evidence_level(record, rtype):
"""Returns uniprot protein existence evidence level for a fasta header.
Evidence levels are 1-5, but we return 5 - x since sorting still demands
that higher is better."""
if rtype != 'swiss':
return -1
for item in record.description.split():
item = item.split('=')
try:
if item[0] == 'PE' and len(item) == 2:
return 5 - int(item[1])
except IndexError:
continue
return -1
<｜fim▁end｜> | return record.description.split(fastadelim)[genefield] |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by keeping only the last one.
"""
records = {acc: (rec, get_record_type(rec)) for acc, rec in
SeqIO.index(fastafn, 'fasta').items()}
proteins = ((x,) for x in records.keys())
sequences = ((acc, str(rec.seq)) for acc, (rec, rtype) in records.items())
desc = ((acc, get_description(rec, rtype)) for acc, (rec, rtype) in records.items() if rtype)
evid = ((acc, get_uniprot_evidence_level(rec, rtype)) for acc, (rec, rtype) in
records.items())
ensgs = [(get_ensg(rec), acc) for acc, (rec, rtype) in records.items()
if rtype == 'ensembl']
def sym_out():
symbols = ((get_symbol(rec, rtype, fastadelim, genefield), acc) for
acc, (rec, rtype) in records.items() if rtype)
othergene = ((get_other_gene(rec, fastadelim, genefield), acc) for acc, (rec, rtype) in records.items()
if not rtype and fastadelim and fastadelim in rec.description)
yield from symbols
yield from othergene
return proteins, sequences, desc, evid, ensgs, [x for x in sym_out()]
def parse_fasta(fn):
with open(fn) as fp:
for record in SeqIO.parse(fp, 'fasta'):
yield record
def get_record_type(record):
dmod = get_decoy_mod_string(record.id)
test_name = record.id
if dmod is not None:
test_name = record.id.replace(dmod, '')
if test_name.split('|')[0] in ['sp', 'tr']:
return 'swiss'
elif test_name[:3] == 'ENS':
return 'ensembl'
else:
return False
def get_decoy_mod_string(protein):
mods = ['tryp_reverse', 'reverse', 'decoy', 'random', 'shuffle']
for mod in mods:
if mod in protein:
if protein.endswith('_{}'.format(mod)):
return '_{}'.format(mod)
elif protein.endswith('{}'.format(mod)):
return mod
elif protein.startswith('{}_'.format(mod)):
return '{}_'.format(mod)
elif protein.startswith('{}'.format(mod)):
return mod
def get_description(record, rectype):
if rectype == 'ensembl':
desc_spl = [x.split(':') for x in record.description.split()]
try:
descix = [ix for ix, x in enumerate(desc_spl) if x[0] == 'description'][0]
except IndexError:
return 'NA'
desc = ' '.join([':'.join(x) for x in desc_spl[descix:]])[12:]
return desc
elif rectype == 'swiss':
desc = []
for part in record.description.split()[1:]:
if len(part.split('=')) > 1:
break
desc.append(part)
return ' '.join(desc)
def get_other_gene(record, fastadelim, genefield):
return record.description.split(fastadelim)[genefield]
def get_genes_pickfdr(fastafn, outputtype, fastadelim, genefield):
"""Called by protein FDR module for both ENSG and e.g. Uniprot"""
for rec in parse_fasta(fastafn):
rtype = get_record_type(rec)
if rtype == 'ensembl' and outputtype == 'ensg':
yield get_ensg(rec)
elif outputtype == 'genename':
yield get_symbol(rec, rtype, fastadelim, genefield)
def get_ensg(record):
fields = [x.split(':') for x in record.description.split()]
try:
return [x[1] for x in fields if x[0] == 'gene' and len(x) == 2][0]
except IndexError:
raise RuntimeError('ENSEMBL detected but cannot find gene ENSG in fasta')
def get_symbol(record, rectype, fastadelim, genefield):
if rectype == 'ensembl':
fields = [x.split(':') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'gene_symbol' and len(x) == 2]
elif rectype == 'swiss':
fields = [x.split('=') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'GN' and len(x) == 2]
elif fastadelim and fastadelim in record.description and genefield:
return record.description.split(fastadelim)[genefield]
else:
<|fim_middle|>
try:
return sym[0]
except IndexError:
return 'NA'
def get_uniprot_evidence_level(record, rtype):
"""Returns uniprot protein existence evidence level for a fasta header.
Evidence levels are 1-5, but we return 5 - x since sorting still demands
that higher is better."""
if rtype != 'swiss':
return -1
for item in record.description.split():
item = item.split('=')
try:
if item[0] == 'PE' and len(item) == 2:
return 5 - int(item[1])
except IndexError:
continue
return -1
<｜fim▁end｜> | return 'NA' |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by keeping only the last one.
"""
records = {acc: (rec, get_record_type(rec)) for acc, rec in
SeqIO.index(fastafn, 'fasta').items()}
proteins = ((x,) for x in records.keys())
sequences = ((acc, str(rec.seq)) for acc, (rec, rtype) in records.items())
desc = ((acc, get_description(rec, rtype)) for acc, (rec, rtype) in records.items() if rtype)
evid = ((acc, get_uniprot_evidence_level(rec, rtype)) for acc, (rec, rtype) in
records.items())
ensgs = [(get_ensg(rec), acc) for acc, (rec, rtype) in records.items()
if rtype == 'ensembl']
def sym_out():
symbols = ((get_symbol(rec, rtype, fastadelim, genefield), acc) for
acc, (rec, rtype) in records.items() if rtype)
othergene = ((get_other_gene(rec, fastadelim, genefield), acc) for acc, (rec, rtype) in records.items()
if not rtype and fastadelim and fastadelim in rec.description)
yield from symbols
yield from othergene
return proteins, sequences, desc, evid, ensgs, [x for x in sym_out()]
def parse_fasta(fn):
with open(fn) as fp:
for record in SeqIO.parse(fp, 'fasta'):
yield record
def get_record_type(record):
dmod = get_decoy_mod_string(record.id)
test_name = record.id
if dmod is not None:
test_name = record.id.replace(dmod, '')
if test_name.split('|')[0] in ['sp', 'tr']:
return 'swiss'
elif test_name[:3] == 'ENS':
return 'ensembl'
else:
return False
def get_decoy_mod_string(protein):
mods = ['tryp_reverse', 'reverse', 'decoy', 'random', 'shuffle']
for mod in mods:
if mod in protein:
if protein.endswith('_{}'.format(mod)):
return '_{}'.format(mod)
elif protein.endswith('{}'.format(mod)):
return mod
elif protein.startswith('{}_'.format(mod)):
return '{}_'.format(mod)
elif protein.startswith('{}'.format(mod)):
return mod
def get_description(record, rectype):
if rectype == 'ensembl':
desc_spl = [x.split(':') for x in record.description.split()]
try:
descix = [ix for ix, x in enumerate(desc_spl) if x[0] == 'description'][0]
except IndexError:
return 'NA'
desc = ' '.join([':'.join(x) for x in desc_spl[descix:]])[12:]
return desc
elif rectype == 'swiss':
desc = []
for part in record.description.split()[1:]:
if len(part.split('=')) > 1:
break
desc.append(part)
return ' '.join(desc)
def get_other_gene(record, fastadelim, genefield):
return record.description.split(fastadelim)[genefield]
def get_genes_pickfdr(fastafn, outputtype, fastadelim, genefield):
"""Called by protein FDR module for both ENSG and e.g. Uniprot"""
for rec in parse_fasta(fastafn):
rtype = get_record_type(rec)
if rtype == 'ensembl' and outputtype == 'ensg':
yield get_ensg(rec)
elif outputtype == 'genename':
yield get_symbol(rec, rtype, fastadelim, genefield)
def get_ensg(record):
fields = [x.split(':') for x in record.description.split()]
try:
return [x[1] for x in fields if x[0] == 'gene' and len(x) == 2][0]
except IndexError:
raise RuntimeError('ENSEMBL detected but cannot find gene ENSG in fasta')
def get_symbol(record, rectype, fastadelim, genefield):
if rectype == 'ensembl':
fields = [x.split(':') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'gene_symbol' and len(x) == 2]
elif rectype == 'swiss':
fields = [x.split('=') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'GN' and len(x) == 2]
elif fastadelim and fastadelim in record.description and genefield:
return record.description.split(fastadelim)[genefield]
else:
return 'NA'
try:
return sym[0]
except IndexError:
return 'NA'
def get_uniprot_evidence_level(record, rtype):
"""Returns uniprot protein existence evidence level for a fasta header.
Evidence levels are 1-5, but we return 5 - x since sorting still demands
that higher is better."""
if rtype != 'swiss':
<|fim_middle|>
for item in record.description.split():
item = item.split('=')
try:
if item[0] == 'PE' and len(item) == 2:
return 5 - int(item[1])
except IndexError:
continue
return -1
<｜fim▁end｜> | return -1 |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by keeping only the last one.
"""
records = {acc: (rec, get_record_type(rec)) for acc, rec in
SeqIO.index(fastafn, 'fasta').items()}
proteins = ((x,) for x in records.keys())
sequences = ((acc, str(rec.seq)) for acc, (rec, rtype) in records.items())
desc = ((acc, get_description(rec, rtype)) for acc, (rec, rtype) in records.items() if rtype)
evid = ((acc, get_uniprot_evidence_level(rec, rtype)) for acc, (rec, rtype) in
records.items())
ensgs = [(get_ensg(rec), acc) for acc, (rec, rtype) in records.items()
if rtype == 'ensembl']
def sym_out():
symbols = ((get_symbol(rec, rtype, fastadelim, genefield), acc) for
acc, (rec, rtype) in records.items() if rtype)
othergene = ((get_other_gene(rec, fastadelim, genefield), acc) for acc, (rec, rtype) in records.items()
if not rtype and fastadelim and fastadelim in rec.description)
yield from symbols
yield from othergene
return proteins, sequences, desc, evid, ensgs, [x for x in sym_out()]
def parse_fasta(fn):
with open(fn) as fp:
for record in SeqIO.parse(fp, 'fasta'):
yield record
def get_record_type(record):
dmod = get_decoy_mod_string(record.id)
test_name = record.id
if dmod is not None:
test_name = record.id.replace(dmod, '')
if test_name.split('|')[0] in ['sp', 'tr']:
return 'swiss'
elif test_name[:3] == 'ENS':
return 'ensembl'
else:
return False
def get_decoy_mod_string(protein):
mods = ['tryp_reverse', 'reverse', 'decoy', 'random', 'shuffle']
for mod in mods:
if mod in protein:
if protein.endswith('_{}'.format(mod)):
return '_{}'.format(mod)
elif protein.endswith('{}'.format(mod)):
return mod
elif protein.startswith('{}_'.format(mod)):
return '{}_'.format(mod)
elif protein.startswith('{}'.format(mod)):
return mod
def get_description(record, rectype):
if rectype == 'ensembl':
desc_spl = [x.split(':') for x in record.description.split()]
try:
descix = [ix for ix, x in enumerate(desc_spl) if x[0] == 'description'][0]
except IndexError:
return 'NA'
desc = ' '.join([':'.join(x) for x in desc_spl[descix:]])[12:]
return desc
elif rectype == 'swiss':
desc = []
for part in record.description.split()[1:]:
if len(part.split('=')) > 1:
break
desc.append(part)
return ' '.join(desc)
def get_other_gene(record, fastadelim, genefield):
return record.description.split(fastadelim)[genefield]
def get_genes_pickfdr(fastafn, outputtype, fastadelim, genefield):
"""Called by protein FDR module for both ENSG and e.g. Uniprot"""
for rec in parse_fasta(fastafn):
rtype = get_record_type(rec)
if rtype == 'ensembl' and outputtype == 'ensg':
yield get_ensg(rec)
elif outputtype == 'genename':
yield get_symbol(rec, rtype, fastadelim, genefield)
def get_ensg(record):
fields = [x.split(':') for x in record.description.split()]
try:
return [x[1] for x in fields if x[0] == 'gene' and len(x) == 2][0]
except IndexError:
raise RuntimeError('ENSEMBL detected but cannot find gene ENSG in fasta')
def get_symbol(record, rectype, fastadelim, genefield):
if rectype == 'ensembl':
fields = [x.split(':') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'gene_symbol' and len(x) == 2]
elif rectype == 'swiss':
fields = [x.split('=') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'GN' and len(x) == 2]
elif fastadelim and fastadelim in record.description and genefield:
return record.description.split(fastadelim)[genefield]
else:
return 'NA'
try:
return sym[0]
except IndexError:
return 'NA'
def get_uniprot_evidence_level(record, rtype):
"""Returns uniprot protein existence evidence level for a fasta header.
Evidence levels are 1-5, but we return 5 - x since sorting still demands
that higher is better."""
if rtype != 'swiss':
return -1
for item in record.description.split():
item = item.split('=')
try:
if item[0] == 'PE' and len(item) == 2:
<|fim_middle|>
except IndexError:
continue
return -1
<｜fim▁end｜> | return 5 - int(item[1]) |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def <|fim_middle|>(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by keeping only the last one.
"""
records = {acc: (rec, get_record_type(rec)) for acc, rec in
SeqIO.index(fastafn, 'fasta').items()}
proteins = ((x,) for x in records.keys())
sequences = ((acc, str(rec.seq)) for acc, (rec, rtype) in records.items())
desc = ((acc, get_description(rec, rtype)) for acc, (rec, rtype) in records.items() if rtype)
evid = ((acc, get_uniprot_evidence_level(rec, rtype)) for acc, (rec, rtype) in
records.items())
ensgs = [(get_ensg(rec), acc) for acc, (rec, rtype) in records.items()
if rtype == 'ensembl']
def sym_out():
symbols = ((get_symbol(rec, rtype, fastadelim, genefield), acc) for
acc, (rec, rtype) in records.items() if rtype)
othergene = ((get_other_gene(rec, fastadelim, genefield), acc) for acc, (rec, rtype) in records.items()
if not rtype and fastadelim and fastadelim in rec.description)
yield from symbols
yield from othergene
return proteins, sequences, desc, evid, ensgs, [x for x in sym_out()]
def parse_fasta(fn):
with open(fn) as fp:
for record in SeqIO.parse(fp, 'fasta'):
yield record
def get_record_type(record):
dmod = get_decoy_mod_string(record.id)
test_name = record.id
if dmod is not None:
test_name = record.id.replace(dmod, '')
if test_name.split('|')[0] in ['sp', 'tr']:
return 'swiss'
elif test_name[:3] == 'ENS':
return 'ensembl'
else:
return False
def get_decoy_mod_string(protein):
mods = ['tryp_reverse', 'reverse', 'decoy', 'random', 'shuffle']
for mod in mods:
if mod in protein:
if protein.endswith('_{}'.format(mod)):
return '_{}'.format(mod)
elif protein.endswith('{}'.format(mod)):
return mod
elif protein.startswith('{}_'.format(mod)):
return '{}_'.format(mod)
elif protein.startswith('{}'.format(mod)):
return mod
def get_description(record, rectype):
if rectype == 'ensembl':
desc_spl = [x.split(':') for x in record.description.split()]
try:
descix = [ix for ix, x in enumerate(desc_spl) if x[0] == 'description'][0]
except IndexError:
return 'NA'
desc = ' '.join([':'.join(x) for x in desc_spl[descix:]])[12:]
return desc
elif rectype == 'swiss':
desc = []
for part in record.description.split()[1:]:
if len(part.split('=')) > 1:
break
desc.append(part)
return ' '.join(desc)
def get_other_gene(record, fastadelim, genefield):
return record.description.split(fastadelim)[genefield]
def get_genes_pickfdr(fastafn, outputtype, fastadelim, genefield):
"""Called by protein FDR module for both ENSG and e.g. Uniprot"""
for rec in parse_fasta(fastafn):
rtype = get_record_type(rec)
if rtype == 'ensembl' and outputtype == 'ensg':
yield get_ensg(rec)
elif outputtype == 'genename':
yield get_symbol(rec, rtype, fastadelim, genefield)
def get_ensg(record):
fields = [x.split(':') for x in record.description.split()]
try:
return [x[1] for x in fields if x[0] == 'gene' and len(x) == 2][0]
except IndexError:
raise RuntimeError('ENSEMBL detected but cannot find gene ENSG in fasta')
def get_symbol(record, rectype, fastadelim, genefield):
if rectype == 'ensembl':
fields = [x.split(':') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'gene_symbol' and len(x) == 2]
elif rectype == 'swiss':
fields = [x.split('=') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'GN' and len(x) == 2]
elif fastadelim and fastadelim in record.description and genefield:
return record.description.split(fastadelim)[genefield]
else:
return 'NA'
try:
return sym[0]
except IndexError:
return 'NA'
def get_uniprot_evidence_level(record, rtype):
"""Returns uniprot protein existence evidence level for a fasta header.
Evidence levels are 1-5, but we return 5 - x since sorting still demands
that higher is better."""
if rtype != 'swiss':
return -1
for item in record.description.split():
item = item.split('=')
try:
if item[0] == 'PE' and len(item) == 2:
return 5 - int(item[1])
except IndexError:
continue
return -1
<｜fim▁end｜> | get_proteins_for_db |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by keeping only the last one.
"""
records = {acc: (rec, get_record_type(rec)) for acc, rec in
SeqIO.index(fastafn, 'fasta').items()}
proteins = ((x,) for x in records.keys())
sequences = ((acc, str(rec.seq)) for acc, (rec, rtype) in records.items())
desc = ((acc, get_description(rec, rtype)) for acc, (rec, rtype) in records.items() if rtype)
evid = ((acc, get_uniprot_evidence_level(rec, rtype)) for acc, (rec, rtype) in
records.items())
ensgs = [(get_ensg(rec), acc) for acc, (rec, rtype) in records.items()
if rtype == 'ensembl']
def <|fim_middle|>():
symbols = ((get_symbol(rec, rtype, fastadelim, genefield), acc) for
acc, (rec, rtype) in records.items() if rtype)
othergene = ((get_other_gene(rec, fastadelim, genefield), acc) for acc, (rec, rtype) in records.items()
if not rtype and fastadelim and fastadelim in rec.description)
yield from symbols
yield from othergene
return proteins, sequences, desc, evid, ensgs, [x for x in sym_out()]
def parse_fasta(fn):
with open(fn) as fp:
for record in SeqIO.parse(fp, 'fasta'):
yield record
def get_record_type(record):
dmod = get_decoy_mod_string(record.id)
test_name = record.id
if dmod is not None:
test_name = record.id.replace(dmod, '')
if test_name.split('|')[0] in ['sp', 'tr']:
return 'swiss'
elif test_name[:3] == 'ENS':
return 'ensembl'
else:
return False
def get_decoy_mod_string(protein):
mods = ['tryp_reverse', 'reverse', 'decoy', 'random', 'shuffle']
for mod in mods:
if mod in protein:
if protein.endswith('_{}'.format(mod)):
return '_{}'.format(mod)
elif protein.endswith('{}'.format(mod)):
return mod
elif protein.startswith('{}_'.format(mod)):
return '{}_'.format(mod)
elif protein.startswith('{}'.format(mod)):
return mod
def get_description(record, rectype):
if rectype == 'ensembl':
desc_spl = [x.split(':') for x in record.description.split()]
try:
descix = [ix for ix, x in enumerate(desc_spl) if x[0] == 'description'][0]
except IndexError:
return 'NA'
desc = ' '.join([':'.join(x) for x in desc_spl[descix:]])[12:]
return desc
elif rectype == 'swiss':
desc = []
for part in record.description.split()[1:]:
if len(part.split('=')) > 1:
break
desc.append(part)
return ' '.join(desc)
def get_other_gene(record, fastadelim, genefield):
return record.description.split(fastadelim)[genefield]
def get_genes_pickfdr(fastafn, outputtype, fastadelim, genefield):
"""Called by protein FDR module for both ENSG and e.g. Uniprot"""
for rec in parse_fasta(fastafn):
rtype = get_record_type(rec)
if rtype == 'ensembl' and outputtype == 'ensg':
yield get_ensg(rec)
elif outputtype == 'genename':
yield get_symbol(rec, rtype, fastadelim, genefield)
def get_ensg(record):
fields = [x.split(':') for x in record.description.split()]
try:
return [x[1] for x in fields if x[0] == 'gene' and len(x) == 2][0]
except IndexError:
raise RuntimeError('ENSEMBL detected but cannot find gene ENSG in fasta')
def get_symbol(record, rectype, fastadelim, genefield):
if rectype == 'ensembl':
fields = [x.split(':') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'gene_symbol' and len(x) == 2]
elif rectype == 'swiss':
fields = [x.split('=') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'GN' and len(x) == 2]
elif fastadelim and fastadelim in record.description and genefield:
return record.description.split(fastadelim)[genefield]
else:
return 'NA'
try:
return sym[0]
except IndexError:
return 'NA'
def get_uniprot_evidence_level(record, rtype):
"""Returns uniprot protein existence evidence level for a fasta header.
Evidence levels are 1-5, but we return 5 - x since sorting still demands
that higher is better."""
if rtype != 'swiss':
return -1
for item in record.description.split():
item = item.split('=')
try:
if item[0] == 'PE' and len(item) == 2:
return 5 - int(item[1])
except IndexError:
continue
return -1
<｜fim▁end｜> | sym_out |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by keeping only the last one.
"""
records = {acc: (rec, get_record_type(rec)) for acc, rec in
SeqIO.index(fastafn, 'fasta').items()}
proteins = ((x,) for x in records.keys())
sequences = ((acc, str(rec.seq)) for acc, (rec, rtype) in records.items())
desc = ((acc, get_description(rec, rtype)) for acc, (rec, rtype) in records.items() if rtype)
evid = ((acc, get_uniprot_evidence_level(rec, rtype)) for acc, (rec, rtype) in
records.items())
ensgs = [(get_ensg(rec), acc) for acc, (rec, rtype) in records.items()
if rtype == 'ensembl']
def sym_out():
symbols = ((get_symbol(rec, rtype, fastadelim, genefield), acc) for
acc, (rec, rtype) in records.items() if rtype)
othergene = ((get_other_gene(rec, fastadelim, genefield), acc) for acc, (rec, rtype) in records.items()
if not rtype and fastadelim and fastadelim in rec.description)
yield from symbols
yield from othergene
return proteins, sequences, desc, evid, ensgs, [x for x in sym_out()]
def <|fim_middle|>(fn):
with open(fn) as fp:
for record in SeqIO.parse(fp, 'fasta'):
yield record
def get_record_type(record):
dmod = get_decoy_mod_string(record.id)
test_name = record.id
if dmod is not None:
test_name = record.id.replace(dmod, '')
if test_name.split('|')[0] in ['sp', 'tr']:
return 'swiss'
elif test_name[:3] == 'ENS':
return 'ensembl'
else:
return False
def get_decoy_mod_string(protein):
mods = ['tryp_reverse', 'reverse', 'decoy', 'random', 'shuffle']
for mod in mods:
if mod in protein:
if protein.endswith('_{}'.format(mod)):
return '_{}'.format(mod)
elif protein.endswith('{}'.format(mod)):
return mod
elif protein.startswith('{}_'.format(mod)):
return '{}_'.format(mod)
elif protein.startswith('{}'.format(mod)):
return mod
def get_description(record, rectype):
if rectype == 'ensembl':
desc_spl = [x.split(':') for x in record.description.split()]
try:
descix = [ix for ix, x in enumerate(desc_spl) if x[0] == 'description'][0]
except IndexError:
return 'NA'
desc = ' '.join([':'.join(x) for x in desc_spl[descix:]])[12:]
return desc
elif rectype == 'swiss':
desc = []
for part in record.description.split()[1:]:
if len(part.split('=')) > 1:
break
desc.append(part)
return ' '.join(desc)
def get_other_gene(record, fastadelim, genefield):
return record.description.split(fastadelim)[genefield]
def get_genes_pickfdr(fastafn, outputtype, fastadelim, genefield):
"""Called by protein FDR module for both ENSG and e.g. Uniprot"""
for rec in parse_fasta(fastafn):
rtype = get_record_type(rec)
if rtype == 'ensembl' and outputtype == 'ensg':
yield get_ensg(rec)
elif outputtype == 'genename':
yield get_symbol(rec, rtype, fastadelim, genefield)
def get_ensg(record):
fields = [x.split(':') for x in record.description.split()]
try:
return [x[1] for x in fields if x[0] == 'gene' and len(x) == 2][0]
except IndexError:
raise RuntimeError('ENSEMBL detected but cannot find gene ENSG in fasta')
def get_symbol(record, rectype, fastadelim, genefield):
if rectype == 'ensembl':
fields = [x.split(':') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'gene_symbol' and len(x) == 2]
elif rectype == 'swiss':
fields = [x.split('=') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'GN' and len(x) == 2]
elif fastadelim and fastadelim in record.description and genefield:
return record.description.split(fastadelim)[genefield]
else:
return 'NA'
try:
return sym[0]
except IndexError:
return 'NA'
def get_uniprot_evidence_level(record, rtype):
"""Returns uniprot protein existence evidence level for a fasta header.
Evidence levels are 1-5, but we return 5 - x since sorting still demands
that higher is better."""
if rtype != 'swiss':
return -1
for item in record.description.split():
item = item.split('=')
try:
if item[0] == 'PE' and len(item) == 2:
return 5 - int(item[1])
except IndexError:
continue
return -1
<｜fim▁end｜> | parse_fasta |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by keeping only the last one.
"""
records = {acc: (rec, get_record_type(rec)) for acc, rec in
SeqIO.index(fastafn, 'fasta').items()}
proteins = ((x,) for x in records.keys())
sequences = ((acc, str(rec.seq)) for acc, (rec, rtype) in records.items())
desc = ((acc, get_description(rec, rtype)) for acc, (rec, rtype) in records.items() if rtype)
evid = ((acc, get_uniprot_evidence_level(rec, rtype)) for acc, (rec, rtype) in
records.items())
ensgs = [(get_ensg(rec), acc) for acc, (rec, rtype) in records.items()
if rtype == 'ensembl']
def sym_out():
symbols = ((get_symbol(rec, rtype, fastadelim, genefield), acc) for
acc, (rec, rtype) in records.items() if rtype)
othergene = ((get_other_gene(rec, fastadelim, genefield), acc) for acc, (rec, rtype) in records.items()
if not rtype and fastadelim and fastadelim in rec.description)
yield from symbols
yield from othergene
return proteins, sequences, desc, evid, ensgs, [x for x in sym_out()]
def parse_fasta(fn):
with open(fn) as fp:
for record in SeqIO.parse(fp, 'fasta'):
yield record
def <|fim_middle|>(record):
dmod = get_decoy_mod_string(record.id)
test_name = record.id
if dmod is not None:
test_name = record.id.replace(dmod, '')
if test_name.split('|')[0] in ['sp', 'tr']:
return 'swiss'
elif test_name[:3] == 'ENS':
return 'ensembl'
else:
return False
def get_decoy_mod_string(protein):
mods = ['tryp_reverse', 'reverse', 'decoy', 'random', 'shuffle']
for mod in mods:
if mod in protein:
if protein.endswith('_{}'.format(mod)):
return '_{}'.format(mod)
elif protein.endswith('{}'.format(mod)):
return mod
elif protein.startswith('{}_'.format(mod)):
return '{}_'.format(mod)
elif protein.startswith('{}'.format(mod)):
return mod
def get_description(record, rectype):
if rectype == 'ensembl':
desc_spl = [x.split(':') for x in record.description.split()]
try:
descix = [ix for ix, x in enumerate(desc_spl) if x[0] == 'description'][0]
except IndexError:
return 'NA'
desc = ' '.join([':'.join(x) for x in desc_spl[descix:]])[12:]
return desc
elif rectype == 'swiss':
desc = []
for part in record.description.split()[1:]:
if len(part.split('=')) > 1:
break
desc.append(part)
return ' '.join(desc)
def get_other_gene(record, fastadelim, genefield):
return record.description.split(fastadelim)[genefield]
def get_genes_pickfdr(fastafn, outputtype, fastadelim, genefield):
"""Called by protein FDR module for both ENSG and e.g. Uniprot"""
for rec in parse_fasta(fastafn):
rtype = get_record_type(rec)
if rtype == 'ensembl' and outputtype == 'ensg':
yield get_ensg(rec)
elif outputtype == 'genename':
yield get_symbol(rec, rtype, fastadelim, genefield)
def get_ensg(record):
fields = [x.split(':') for x in record.description.split()]
try:
return [x[1] for x in fields if x[0] == 'gene' and len(x) == 2][0]
except IndexError:
raise RuntimeError('ENSEMBL detected but cannot find gene ENSG in fasta')
def get_symbol(record, rectype, fastadelim, genefield):
if rectype == 'ensembl':
fields = [x.split(':') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'gene_symbol' and len(x) == 2]
elif rectype == 'swiss':
fields = [x.split('=') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'GN' and len(x) == 2]
elif fastadelim and fastadelim in record.description and genefield:
return record.description.split(fastadelim)[genefield]
else:
return 'NA'
try:
return sym[0]
except IndexError:
return 'NA'
def get_uniprot_evidence_level(record, rtype):
"""Returns uniprot protein existence evidence level for a fasta header.
Evidence levels are 1-5, but we return 5 - x since sorting still demands
that higher is better."""
if rtype != 'swiss':
return -1
for item in record.description.split():
item = item.split('=')
try:
if item[0] == 'PE' and len(item) == 2:
return 5 - int(item[1])
except IndexError:
continue
return -1
<｜fim▁end｜> | get_record_type |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by keeping only the last one.
"""
records = {acc: (rec, get_record_type(rec)) for acc, rec in
SeqIO.index(fastafn, 'fasta').items()}
proteins = ((x,) for x in records.keys())
sequences = ((acc, str(rec.seq)) for acc, (rec, rtype) in records.items())
desc = ((acc, get_description(rec, rtype)) for acc, (rec, rtype) in records.items() if rtype)
evid = ((acc, get_uniprot_evidence_level(rec, rtype)) for acc, (rec, rtype) in
records.items())
ensgs = [(get_ensg(rec), acc) for acc, (rec, rtype) in records.items()
if rtype == 'ensembl']
def sym_out():
symbols = ((get_symbol(rec, rtype, fastadelim, genefield), acc) for
acc, (rec, rtype) in records.items() if rtype)
othergene = ((get_other_gene(rec, fastadelim, genefield), acc) for acc, (rec, rtype) in records.items()
if not rtype and fastadelim and fastadelim in rec.description)
yield from symbols
yield from othergene
return proteins, sequences, desc, evid, ensgs, [x for x in sym_out()]
def parse_fasta(fn):
with open(fn) as fp:
for record in SeqIO.parse(fp, 'fasta'):
yield record
def get_record_type(record):
dmod = get_decoy_mod_string(record.id)
test_name = record.id
if dmod is not None:
test_name = record.id.replace(dmod, '')
if test_name.split('|')[0] in ['sp', 'tr']:
return 'swiss'
elif test_name[:3] == 'ENS':
return 'ensembl'
else:
return False
def <|fim_middle|>(protein):
mods = ['tryp_reverse', 'reverse', 'decoy', 'random', 'shuffle']
for mod in mods:
if mod in protein:
if protein.endswith('_{}'.format(mod)):
return '_{}'.format(mod)
elif protein.endswith('{}'.format(mod)):
return mod
elif protein.startswith('{}_'.format(mod)):
return '{}_'.format(mod)
elif protein.startswith('{}'.format(mod)):
return mod
def get_description(record, rectype):
if rectype == 'ensembl':
desc_spl = [x.split(':') for x in record.description.split()]
try:
descix = [ix for ix, x in enumerate(desc_spl) if x[0] == 'description'][0]
except IndexError:
return 'NA'
desc = ' '.join([':'.join(x) for x in desc_spl[descix:]])[12:]
return desc
elif rectype == 'swiss':
desc = []
for part in record.description.split()[1:]:
if len(part.split('=')) > 1:
break
desc.append(part)
return ' '.join(desc)
def get_other_gene(record, fastadelim, genefield):
return record.description.split(fastadelim)[genefield]
def get_genes_pickfdr(fastafn, outputtype, fastadelim, genefield):
"""Called by protein FDR module for both ENSG and e.g. Uniprot"""
for rec in parse_fasta(fastafn):
rtype = get_record_type(rec)
if rtype == 'ensembl' and outputtype == 'ensg':
yield get_ensg(rec)
elif outputtype == 'genename':
yield get_symbol(rec, rtype, fastadelim, genefield)
def get_ensg(record):
fields = [x.split(':') for x in record.description.split()]
try:
return [x[1] for x in fields if x[0] == 'gene' and len(x) == 2][0]
except IndexError:
raise RuntimeError('ENSEMBL detected but cannot find gene ENSG in fasta')
def get_symbol(record, rectype, fastadelim, genefield):
if rectype == 'ensembl':
fields = [x.split(':') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'gene_symbol' and len(x) == 2]
elif rectype == 'swiss':
fields = [x.split('=') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'GN' and len(x) == 2]
elif fastadelim and fastadelim in record.description and genefield:
return record.description.split(fastadelim)[genefield]
else:
return 'NA'
try:
return sym[0]
except IndexError:
return 'NA'
def get_uniprot_evidence_level(record, rtype):
"""Returns uniprot protein existence evidence level for a fasta header.
Evidence levels are 1-5, but we return 5 - x since sorting still demands
that higher is better."""
if rtype != 'swiss':
return -1
for item in record.description.split():
item = item.split('=')
try:
if item[0] == 'PE' and len(item) == 2:
return 5 - int(item[1])
except IndexError:
continue
return -1
<｜fim▁end｜> | get_decoy_mod_string |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by keeping only the last one.
"""
records = {acc: (rec, get_record_type(rec)) for acc, rec in
SeqIO.index(fastafn, 'fasta').items()}
proteins = ((x,) for x in records.keys())
sequences = ((acc, str(rec.seq)) for acc, (rec, rtype) in records.items())
desc = ((acc, get_description(rec, rtype)) for acc, (rec, rtype) in records.items() if rtype)
evid = ((acc, get_uniprot_evidence_level(rec, rtype)) for acc, (rec, rtype) in
records.items())
ensgs = [(get_ensg(rec), acc) for acc, (rec, rtype) in records.items()
if rtype == 'ensembl']
def sym_out():
symbols = ((get_symbol(rec, rtype, fastadelim, genefield), acc) for
acc, (rec, rtype) in records.items() if rtype)
othergene = ((get_other_gene(rec, fastadelim, genefield), acc) for acc, (rec, rtype) in records.items()
if not rtype and fastadelim and fastadelim in rec.description)
yield from symbols
yield from othergene
return proteins, sequences, desc, evid, ensgs, [x for x in sym_out()]
def parse_fasta(fn):
with open(fn) as fp:
for record in SeqIO.parse(fp, 'fasta'):
yield record
def get_record_type(record):
dmod = get_decoy_mod_string(record.id)
test_name = record.id
if dmod is not None:
test_name = record.id.replace(dmod, '')
if test_name.split('|')[0] in ['sp', 'tr']:
return 'swiss'
elif test_name[:3] == 'ENS':
return 'ensembl'
else:
return False
def get_decoy_mod_string(protein):
mods = ['tryp_reverse', 'reverse', 'decoy', 'random', 'shuffle']
for mod in mods:
if mod in protein:
if protein.endswith('_{}'.format(mod)):
return '_{}'.format(mod)
elif protein.endswith('{}'.format(mod)):
return mod
elif protein.startswith('{}_'.format(mod)):
return '{}_'.format(mod)
elif protein.startswith('{}'.format(mod)):
return mod
def <|fim_middle|>(record, rectype):
if rectype == 'ensembl':
desc_spl = [x.split(':') for x in record.description.split()]
try:
descix = [ix for ix, x in enumerate(desc_spl) if x[0] == 'description'][0]
except IndexError:
return 'NA'
desc = ' '.join([':'.join(x) for x in desc_spl[descix:]])[12:]
return desc
elif rectype == 'swiss':
desc = []
for part in record.description.split()[1:]:
if len(part.split('=')) > 1:
break
desc.append(part)
return ' '.join(desc)
def get_other_gene(record, fastadelim, genefield):
return record.description.split(fastadelim)[genefield]
def get_genes_pickfdr(fastafn, outputtype, fastadelim, genefield):
"""Called by protein FDR module for both ENSG and e.g. Uniprot"""
for rec in parse_fasta(fastafn):
rtype = get_record_type(rec)
if rtype == 'ensembl' and outputtype == 'ensg':
yield get_ensg(rec)
elif outputtype == 'genename':
yield get_symbol(rec, rtype, fastadelim, genefield)
def get_ensg(record):
fields = [x.split(':') for x in record.description.split()]
try:
return [x[1] for x in fields if x[0] == 'gene' and len(x) == 2][0]
except IndexError:
raise RuntimeError('ENSEMBL detected but cannot find gene ENSG in fasta')
def get_symbol(record, rectype, fastadelim, genefield):
if rectype == 'ensembl':
fields = [x.split(':') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'gene_symbol' and len(x) == 2]
elif rectype == 'swiss':
fields = [x.split('=') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'GN' and len(x) == 2]
elif fastadelim and fastadelim in record.description and genefield:
return record.description.split(fastadelim)[genefield]
else:
return 'NA'
try:
return sym[0]
except IndexError:
return 'NA'
def get_uniprot_evidence_level(record, rtype):
"""Returns uniprot protein existence evidence level for a fasta header.
Evidence levels are 1-5, but we return 5 - x since sorting still demands
that higher is better."""
if rtype != 'swiss':
return -1
for item in record.description.split():
item = item.split('=')
try:
if item[0] == 'PE' and len(item) == 2:
return 5 - int(item[1])
except IndexError:
continue
return -1
<｜fim▁end｜> | get_description |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by keeping only the last one.
"""
records = {acc: (rec, get_record_type(rec)) for acc, rec in
SeqIO.index(fastafn, 'fasta').items()}
proteins = ((x,) for x in records.keys())
sequences = ((acc, str(rec.seq)) for acc, (rec, rtype) in records.items())
desc = ((acc, get_description(rec, rtype)) for acc, (rec, rtype) in records.items() if rtype)
evid = ((acc, get_uniprot_evidence_level(rec, rtype)) for acc, (rec, rtype) in
records.items())
ensgs = [(get_ensg(rec), acc) for acc, (rec, rtype) in records.items()
if rtype == 'ensembl']
def sym_out():
symbols = ((get_symbol(rec, rtype, fastadelim, genefield), acc) for
acc, (rec, rtype) in records.items() if rtype)
othergene = ((get_other_gene(rec, fastadelim, genefield), acc) for acc, (rec, rtype) in records.items()
if not rtype and fastadelim and fastadelim in rec.description)
yield from symbols
yield from othergene
return proteins, sequences, desc, evid, ensgs, [x for x in sym_out()]
def parse_fasta(fn):
with open(fn) as fp:
for record in SeqIO.parse(fp, 'fasta'):
yield record
def get_record_type(record):
dmod = get_decoy_mod_string(record.id)
test_name = record.id
if dmod is not None:
test_name = record.id.replace(dmod, '')
if test_name.split('|')[0] in ['sp', 'tr']:
return 'swiss'
elif test_name[:3] == 'ENS':
return 'ensembl'
else:
return False
def get_decoy_mod_string(protein):
mods = ['tryp_reverse', 'reverse', 'decoy', 'random', 'shuffle']
for mod in mods:
if mod in protein:
if protein.endswith('_{}'.format(mod)):
return '_{}'.format(mod)
elif protein.endswith('{}'.format(mod)):
return mod
elif protein.startswith('{}_'.format(mod)):
return '{}_'.format(mod)
elif protein.startswith('{}'.format(mod)):
return mod
def get_description(record, rectype):
if rectype == 'ensembl':
desc_spl = [x.split(':') for x in record.description.split()]
try:
descix = [ix for ix, x in enumerate(desc_spl) if x[0] == 'description'][0]
except IndexError:
return 'NA'
desc = ' '.join([':'.join(x) for x in desc_spl[descix:]])[12:]
return desc
elif rectype == 'swiss':
desc = []
for part in record.description.split()[1:]:
if len(part.split('=')) > 1:
break
desc.append(part)
return ' '.join(desc)
def <|fim_middle|>(record, fastadelim, genefield):
return record.description.split(fastadelim)[genefield]
def get_genes_pickfdr(fastafn, outputtype, fastadelim, genefield):
"""Called by protein FDR module for both ENSG and e.g. Uniprot"""
for rec in parse_fasta(fastafn):
rtype = get_record_type(rec)
if rtype == 'ensembl' and outputtype == 'ensg':
yield get_ensg(rec)
elif outputtype == 'genename':
yield get_symbol(rec, rtype, fastadelim, genefield)
def get_ensg(record):
fields = [x.split(':') for x in record.description.split()]
try:
return [x[1] for x in fields if x[0] == 'gene' and len(x) == 2][0]
except IndexError:
raise RuntimeError('ENSEMBL detected but cannot find gene ENSG in fasta')
def get_symbol(record, rectype, fastadelim, genefield):
if rectype == 'ensembl':
fields = [x.split(':') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'gene_symbol' and len(x) == 2]
elif rectype == 'swiss':
fields = [x.split('=') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'GN' and len(x) == 2]
elif fastadelim and fastadelim in record.description and genefield:
return record.description.split(fastadelim)[genefield]
else:
return 'NA'
try:
return sym[0]
except IndexError:
return 'NA'
def get_uniprot_evidence_level(record, rtype):
"""Returns uniprot protein existence evidence level for a fasta header.
Evidence levels are 1-5, but we return 5 - x since sorting still demands
that higher is better."""
if rtype != 'swiss':
return -1
for item in record.description.split():
item = item.split('=')
try:
if item[0] == 'PE' and len(item) == 2:
return 5 - int(item[1])
except IndexError:
continue
return -1
<｜fim▁end｜> | get_other_gene |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by keeping only the last one.
"""
records = {acc: (rec, get_record_type(rec)) for acc, rec in
SeqIO.index(fastafn, 'fasta').items()}
proteins = ((x,) for x in records.keys())
sequences = ((acc, str(rec.seq)) for acc, (rec, rtype) in records.items())
desc = ((acc, get_description(rec, rtype)) for acc, (rec, rtype) in records.items() if rtype)
evid = ((acc, get_uniprot_evidence_level(rec, rtype)) for acc, (rec, rtype) in
records.items())
ensgs = [(get_ensg(rec), acc) for acc, (rec, rtype) in records.items()
if rtype == 'ensembl']
def sym_out():
symbols = ((get_symbol(rec, rtype, fastadelim, genefield), acc) for
acc, (rec, rtype) in records.items() if rtype)
othergene = ((get_other_gene(rec, fastadelim, genefield), acc) for acc, (rec, rtype) in records.items()
if not rtype and fastadelim and fastadelim in rec.description)
yield from symbols
yield from othergene
return proteins, sequences, desc, evid, ensgs, [x for x in sym_out()]
def parse_fasta(fn):
with open(fn) as fp:
for record in SeqIO.parse(fp, 'fasta'):
yield record
def get_record_type(record):
dmod = get_decoy_mod_string(record.id)
test_name = record.id
if dmod is not None:
test_name = record.id.replace(dmod, '')
if test_name.split('|')[0] in ['sp', 'tr']:
return 'swiss'
elif test_name[:3] == 'ENS':
return 'ensembl'
else:
return False
def get_decoy_mod_string(protein):
mods = ['tryp_reverse', 'reverse', 'decoy', 'random', 'shuffle']
for mod in mods:
if mod in protein:
if protein.endswith('_{}'.format(mod)):
return '_{}'.format(mod)
elif protein.endswith('{}'.format(mod)):
return mod
elif protein.startswith('{}_'.format(mod)):
return '{}_'.format(mod)
elif protein.startswith('{}'.format(mod)):
return mod
def get_description(record, rectype):
if rectype == 'ensembl':
desc_spl = [x.split(':') for x in record.description.split()]
try:
descix = [ix for ix, x in enumerate(desc_spl) if x[0] == 'description'][0]
except IndexError:
return 'NA'
desc = ' '.join([':'.join(x) for x in desc_spl[descix:]])[12:]
return desc
elif rectype == 'swiss':
desc = []
for part in record.description.split()[1:]:
if len(part.split('=')) > 1:
break
desc.append(part)
return ' '.join(desc)
def get_other_gene(record, fastadelim, genefield):
return record.description.split(fastadelim)[genefield]
def <|fim_middle|>(fastafn, outputtype, fastadelim, genefield):
"""Called by protein FDR module for both ENSG and e.g. Uniprot"""
for rec in parse_fasta(fastafn):
rtype = get_record_type(rec)
if rtype == 'ensembl' and outputtype == 'ensg':
yield get_ensg(rec)
elif outputtype == 'genename':
yield get_symbol(rec, rtype, fastadelim, genefield)
def get_ensg(record):
fields = [x.split(':') for x in record.description.split()]
try:
return [x[1] for x in fields if x[0] == 'gene' and len(x) == 2][0]
except IndexError:
raise RuntimeError('ENSEMBL detected but cannot find gene ENSG in fasta')
def get_symbol(record, rectype, fastadelim, genefield):
if rectype == 'ensembl':
fields = [x.split(':') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'gene_symbol' and len(x) == 2]
elif rectype == 'swiss':
fields = [x.split('=') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'GN' and len(x) == 2]
elif fastadelim and fastadelim in record.description and genefield:
return record.description.split(fastadelim)[genefield]
else:
return 'NA'
try:
return sym[0]
except IndexError:
return 'NA'
def get_uniprot_evidence_level(record, rtype):
"""Returns uniprot protein existence evidence level for a fasta header.
Evidence levels are 1-5, but we return 5 - x since sorting still demands
that higher is better."""
if rtype != 'swiss':
return -1
for item in record.description.split():
item = item.split('=')
try:
if item[0] == 'PE' and len(item) == 2:
return 5 - int(item[1])
except IndexError:
continue
return -1
<｜fim▁end｜> | get_genes_pickfdr |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by keeping only the last one.
"""
records = {acc: (rec, get_record_type(rec)) for acc, rec in
SeqIO.index(fastafn, 'fasta').items()}
proteins = ((x,) for x in records.keys())
sequences = ((acc, str(rec.seq)) for acc, (rec, rtype) in records.items())
desc = ((acc, get_description(rec, rtype)) for acc, (rec, rtype) in records.items() if rtype)
evid = ((acc, get_uniprot_evidence_level(rec, rtype)) for acc, (rec, rtype) in
records.items())
ensgs = [(get_ensg(rec), acc) for acc, (rec, rtype) in records.items()
if rtype == 'ensembl']
def sym_out():
symbols = ((get_symbol(rec, rtype, fastadelim, genefield), acc) for
acc, (rec, rtype) in records.items() if rtype)
othergene = ((get_other_gene(rec, fastadelim, genefield), acc) for acc, (rec, rtype) in records.items()
if not rtype and fastadelim and fastadelim in rec.description)
yield from symbols
yield from othergene
return proteins, sequences, desc, evid, ensgs, [x for x in sym_out()]
def parse_fasta(fn):
with open(fn) as fp:
for record in SeqIO.parse(fp, 'fasta'):
yield record
def get_record_type(record):
dmod = get_decoy_mod_string(record.id)
test_name = record.id
if dmod is not None:
test_name = record.id.replace(dmod, '')
if test_name.split('|')[0] in ['sp', 'tr']:
return 'swiss'
elif test_name[:3] == 'ENS':
return 'ensembl'
else:
return False
def get_decoy_mod_string(protein):
mods = ['tryp_reverse', 'reverse', 'decoy', 'random', 'shuffle']
for mod in mods:
if mod in protein:
if protein.endswith('_{}'.format(mod)):
return '_{}'.format(mod)
elif protein.endswith('{}'.format(mod)):
return mod
elif protein.startswith('{}_'.format(mod)):
return '{}_'.format(mod)
elif protein.startswith('{}'.format(mod)):
return mod
def get_description(record, rectype):
if rectype == 'ensembl':
desc_spl = [x.split(':') for x in record.description.split()]
try:
descix = [ix for ix, x in enumerate(desc_spl) if x[0] == 'description'][0]
except IndexError:
return 'NA'
desc = ' '.join([':'.join(x) for x in desc_spl[descix:]])[12:]
return desc
elif rectype == 'swiss':
desc = []
for part in record.description.split()[1:]:
if len(part.split('=')) > 1:
break
desc.append(part)
return ' '.join(desc)
def get_other_gene(record, fastadelim, genefield):
return record.description.split(fastadelim)[genefield]
def get_genes_pickfdr(fastafn, outputtype, fastadelim, genefield):
"""Called by protein FDR module for both ENSG and e.g. Uniprot"""
for rec in parse_fasta(fastafn):
rtype = get_record_type(rec)
if rtype == 'ensembl' and outputtype == 'ensg':
yield get_ensg(rec)
elif outputtype == 'genename':
yield get_symbol(rec, rtype, fastadelim, genefield)
def <|fim_middle|>(record):
fields = [x.split(':') for x in record.description.split()]
try:
return [x[1] for x in fields if x[0] == 'gene' and len(x) == 2][0]
except IndexError:
raise RuntimeError('ENSEMBL detected but cannot find gene ENSG in fasta')
def get_symbol(record, rectype, fastadelim, genefield):
if rectype == 'ensembl':
fields = [x.split(':') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'gene_symbol' and len(x) == 2]
elif rectype == 'swiss':
fields = [x.split('=') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'GN' and len(x) == 2]
elif fastadelim and fastadelim in record.description and genefield:
return record.description.split(fastadelim)[genefield]
else:
return 'NA'
try:
return sym[0]
except IndexError:
return 'NA'
def get_uniprot_evidence_level(record, rtype):
"""Returns uniprot protein existence evidence level for a fasta header.
Evidence levels are 1-5, but we return 5 - x since sorting still demands
that higher is better."""
if rtype != 'swiss':
return -1
for item in record.description.split():
item = item.split('=')
try:
if item[0] == 'PE' and len(item) == 2:
return 5 - int(item[1])
except IndexError:
continue
return -1
<｜fim▁end｜> | get_ensg |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by keeping only the last one.
"""
records = {acc: (rec, get_record_type(rec)) for acc, rec in
SeqIO.index(fastafn, 'fasta').items()}
proteins = ((x,) for x in records.keys())
sequences = ((acc, str(rec.seq)) for acc, (rec, rtype) in records.items())
desc = ((acc, get_description(rec, rtype)) for acc, (rec, rtype) in records.items() if rtype)
evid = ((acc, get_uniprot_evidence_level(rec, rtype)) for acc, (rec, rtype) in
records.items())
ensgs = [(get_ensg(rec), acc) for acc, (rec, rtype) in records.items()
if rtype == 'ensembl']
def sym_out():
symbols = ((get_symbol(rec, rtype, fastadelim, genefield), acc) for
acc, (rec, rtype) in records.items() if rtype)
othergene = ((get_other_gene(rec, fastadelim, genefield), acc) for acc, (rec, rtype) in records.items()
if not rtype and fastadelim and fastadelim in rec.description)
yield from symbols
yield from othergene
return proteins, sequences, desc, evid, ensgs, [x for x in sym_out()]
def parse_fasta(fn):
with open(fn) as fp:
for record in SeqIO.parse(fp, 'fasta'):
yield record
def get_record_type(record):
dmod = get_decoy_mod_string(record.id)
test_name = record.id
if dmod is not None:
test_name = record.id.replace(dmod, '')
if test_name.split('|')[0] in ['sp', 'tr']:
return 'swiss'
elif test_name[:3] == 'ENS':
return 'ensembl'
else:
return False
def get_decoy_mod_string(protein):
mods = ['tryp_reverse', 'reverse', 'decoy', 'random', 'shuffle']
for mod in mods:
if mod in protein:
if protein.endswith('_{}'.format(mod)):
return '_{}'.format(mod)
elif protein.endswith('{}'.format(mod)):
return mod
elif protein.startswith('{}_'.format(mod)):
return '{}_'.format(mod)
elif protein.startswith('{}'.format(mod)):
return mod
def get_description(record, rectype):
if rectype == 'ensembl':
desc_spl = [x.split(':') for x in record.description.split()]
try:
descix = [ix for ix, x in enumerate(desc_spl) if x[0] == 'description'][0]
except IndexError:
return 'NA'
desc = ' '.join([':'.join(x) for x in desc_spl[descix:]])[12:]
return desc
elif rectype == 'swiss':
desc = []
for part in record.description.split()[1:]:
if len(part.split('=')) > 1:
break
desc.append(part)
return ' '.join(desc)
def get_other_gene(record, fastadelim, genefield):
return record.description.split(fastadelim)[genefield]
def get_genes_pickfdr(fastafn, outputtype, fastadelim, genefield):
"""Called by protein FDR module for both ENSG and e.g. Uniprot"""
for rec in parse_fasta(fastafn):
rtype = get_record_type(rec)
if rtype == 'ensembl' and outputtype == 'ensg':
yield get_ensg(rec)
elif outputtype == 'genename':
yield get_symbol(rec, rtype, fastadelim, genefield)
def get_ensg(record):
fields = [x.split(':') for x in record.description.split()]
try:
return [x[1] for x in fields if x[0] == 'gene' and len(x) == 2][0]
except IndexError:
raise RuntimeError('ENSEMBL detected but cannot find gene ENSG in fasta')
def <|fim_middle|>(record, rectype, fastadelim, genefield):
if rectype == 'ensembl':
fields = [x.split(':') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'gene_symbol' and len(x) == 2]
elif rectype == 'swiss':
fields = [x.split('=') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'GN' and len(x) == 2]
elif fastadelim and fastadelim in record.description and genefield:
return record.description.split(fastadelim)[genefield]
else:
return 'NA'
try:
return sym[0]
except IndexError:
return 'NA'
def get_uniprot_evidence_level(record, rtype):
"""Returns uniprot protein existence evidence level for a fasta header.
Evidence levels are 1-5, but we return 5 - x since sorting still demands
that higher is better."""
if rtype != 'swiss':
return -1
for item in record.description.split():
item = item.split('=')
try:
if item[0] == 'PE' and len(item) == 2:
return 5 - int(item[1])
except IndexError:
continue
return -1
<｜fim▁end｜> | get_symbol |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by keeping only the last one.
"""
records = {acc: (rec, get_record_type(rec)) for acc, rec in
SeqIO.index(fastafn, 'fasta').items()}
proteins = ((x,) for x in records.keys())
sequences = ((acc, str(rec.seq)) for acc, (rec, rtype) in records.items())
desc = ((acc, get_description(rec, rtype)) for acc, (rec, rtype) in records.items() if rtype)
evid = ((acc, get_uniprot_evidence_level(rec, rtype)) for acc, (rec, rtype) in
records.items())
ensgs = [(get_ensg(rec), acc) for acc, (rec, rtype) in records.items()
if rtype == 'ensembl']
def sym_out():
symbols = ((get_symbol(rec, rtype, fastadelim, genefield), acc) for
acc, (rec, rtype) in records.items() if rtype)
othergene = ((get_other_gene(rec, fastadelim, genefield), acc) for acc, (rec, rtype) in records.items()
if not rtype and fastadelim and fastadelim in rec.description)
yield from symbols
yield from othergene
return proteins, sequences, desc, evid, ensgs, [x for x in sym_out()]
def parse_fasta(fn):
with open(fn) as fp:
for record in SeqIO.parse(fp, 'fasta'):
yield record
def get_record_type(record):
dmod = get_decoy_mod_string(record.id)
test_name = record.id
if dmod is not None:
test_name = record.id.replace(dmod, '')
if test_name.split('|')[0] in ['sp', 'tr']:
return 'swiss'
elif test_name[:3] == 'ENS':
return 'ensembl'
else:
return False
def get_decoy_mod_string(protein):
mods = ['tryp_reverse', 'reverse', 'decoy', 'random', 'shuffle']
for mod in mods:
if mod in protein:
if protein.endswith('_{}'.format(mod)):
return '_{}'.format(mod)
elif protein.endswith('{}'.format(mod)):
return mod
elif protein.startswith('{}_'.format(mod)):
return '{}_'.format(mod)
elif protein.startswith('{}'.format(mod)):
return mod
def get_description(record, rectype):
if rectype == 'ensembl':
desc_spl = [x.split(':') for x in record.description.split()]
try:
descix = [ix for ix, x in enumerate(desc_spl) if x[0] == 'description'][0]
except IndexError:
return 'NA'
desc = ' '.join([':'.join(x) for x in desc_spl[descix:]])[12:]
return desc
elif rectype == 'swiss':
desc = []
for part in record.description.split()[1:]:
if len(part.split('=')) > 1:
break
desc.append(part)
return ' '.join(desc)
def get_other_gene(record, fastadelim, genefield):
return record.description.split(fastadelim)[genefield]
def get_genes_pickfdr(fastafn, outputtype, fastadelim, genefield):
"""Called by protein FDR module for both ENSG and e.g. Uniprot"""
for rec in parse_fasta(fastafn):
rtype = get_record_type(rec)
if rtype == 'ensembl' and outputtype == 'ensg':
yield get_ensg(rec)
elif outputtype == 'genename':
yield get_symbol(rec, rtype, fastadelim, genefield)
def get_ensg(record):
fields = [x.split(':') for x in record.description.split()]
try:
return [x[1] for x in fields if x[0] == 'gene' and len(x) == 2][0]
except IndexError:
raise RuntimeError('ENSEMBL detected but cannot find gene ENSG in fasta')
def get_symbol(record, rectype, fastadelim, genefield):
if rectype == 'ensembl':
fields = [x.split(':') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'gene_symbol' and len(x) == 2]
elif rectype == 'swiss':
fields = [x.split('=') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'GN' and len(x) == 2]
elif fastadelim and fastadelim in record.description and genefield:
return record.description.split(fastadelim)[genefield]
else:
return 'NA'
try:
return sym[0]
except IndexError:
return 'NA'
def <|fim_middle|>(record, rtype):
"""Returns uniprot protein existence evidence level for a fasta header.
Evidence levels are 1-5, but we return 5 - x since sorting still demands
that higher is better."""
if rtype != 'swiss':
return -1
for item in record.description.split():
item = item.split('=')
try:
if item[0] == 'PE' and len(item) == 2:
return 5 - int(item[1])
except IndexError:
continue
return -1
<｜fim▁end｜> | get_uniprot_evidence_level |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
from . import parser
class Rule(parser.Parser):
def __init__(self, expected_attr_type=None):
self.__expected_attr_type = expected_attr_type
@property
def attr_type(self):
if self.__expected_attr_type:
return self.__expected_attr_type
else:
try:
inner_parser = self.__parser
except AttributeError:
raise NotImplementedError
else:
return inner_parser.attr_type
@property
def parser(self):
return self.__parser
@parser.setter
def parser(self, value):
if self.__expected_attr_type and self.__expected_attr_type != value.attr_type:<｜fim▁hole｜> raise ValueError('Unexpected attribute type')
self.__parser = parser.as_parser(value)
def _parse(self, state, *args, **kwargs):
with state.open_scope(*args, **kwargs):
self.__parser._parse(state)
def __imod__(self, other):
self.parser = other
return self
def __call__(self, *args, **kwargs):
return RuleCall(self, *args, **kwargs)
class RuleCall(parser.Unary):
def __init__(self, rule, *args, **kwargs):
if not isinstance(rule, Rule):
raise TypeError('Expected rule to be type Rule, was {}'.format(type(rule).__name__))
super(RuleCall, self).__init__(rule)
self.__args = args
self.__kwargs = kwargs
@property
def args(self):
return self.__args
@property
def kwargs(self):
return dict(self.__kwargs)
def _parse(self, state):
args = [state.invoke(a) for a in self.__args]
kwargs = {k: state.invoke(v) for k, v in self.__kwargs.items()}
self.parser._parse(state, *args, **kwargs)<｜fim▁end｜> | |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
from . import parser
class Rule(parser.Parser):
<|fim_middle|>
class RuleCall(parser.Unary):
def __init__(self, rule, *args, **kwargs):
if not isinstance(rule, Rule):
raise TypeError('Expected rule to be type Rule, was {}'.format(type(rule).__name__))
super(RuleCall, self).__init__(rule)
self.__args = args
self.__kwargs = kwargs
@property
def args(self):
return self.__args
@property
def kwargs(self):
return dict(self.__kwargs)
def _parse(self, state):
args = [state.invoke(a) for a in self.__args]
kwargs = {k: state.invoke(v) for k, v in self.__kwargs.items()}
self.parser._parse(state, *args, **kwargs)
<｜fim▁end｜> | def __init__(self, expected_attr_type=None):
self.__expected_attr_type = expected_attr_type
@property
def attr_type(self):
if self.__expected_attr_type:
return self.__expected_attr_type
else:
try:
inner_parser = self.__parser
except AttributeError:
raise NotImplementedError
else:
return inner_parser.attr_type
@property
def parser(self):
return self.__parser
@parser.setter
def parser(self, value):
if self.__expected_attr_type and self.__expected_attr_type != value.attr_type:
raise ValueError('Unexpected attribute type')
self.__parser = parser.as_parser(value)
def _parse(self, state, *args, **kwargs):
with state.open_scope(*args, **kwargs):
self.__parser._parse(state)
def __imod__(self, other):
self.parser = other
return self
def __call__(self, *args, **kwargs):
return RuleCall(self, *args, **kwargs) |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
from . import parser
class Rule(parser.Parser):
def __init__(self, expected_attr_type=None):
<|fim_middle|>
@property
def attr_type(self):
if self.__expected_attr_type:
return self.__expected_attr_type
else:
try:
inner_parser = self.__parser
except AttributeError:
raise NotImplementedError
else:
return inner_parser.attr_type
@property
def parser(self):
return self.__parser
@parser.setter
def parser(self, value):
if self.__expected_attr_type and self.__expected_attr_type != value.attr_type:
raise ValueError('Unexpected attribute type')
self.__parser = parser.as_parser(value)
def _parse(self, state, *args, **kwargs):
with state.open_scope(*args, **kwargs):
self.__parser._parse(state)
def __imod__(self, other):
self.parser = other
return self
def __call__(self, *args, **kwargs):
return RuleCall(self, *args, **kwargs)
class RuleCall(parser.Unary):
def __init__(self, rule, *args, **kwargs):
if not isinstance(rule, Rule):
raise TypeError('Expected rule to be type Rule, was {}'.format(type(rule).__name__))
super(RuleCall, self).__init__(rule)
self.__args = args
self.__kwargs = kwargs
@property
def args(self):
return self.__args
@property
def kwargs(self):
return dict(self.__kwargs)
def _parse(self, state):
args = [state.invoke(a) for a in self.__args]
kwargs = {k: state.invoke(v) for k, v in self.__kwargs.items()}
self.parser._parse(state, *args, **kwargs)
<｜fim▁end｜> | self.__expected_attr_type = expected_attr_type |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
from . import parser
class Rule(parser.Parser):
def __init__(self, expected_attr_type=None):
self.__expected_attr_type = expected_attr_type
@property
def attr_type(self):
<|fim_middle|>
@property
def parser(self):
return self.__parser
@parser.setter
def parser(self, value):
if self.__expected_attr_type and self.__expected_attr_type != value.attr_type:
raise ValueError('Unexpected attribute type')
self.__parser = parser.as_parser(value)
def _parse(self, state, *args, **kwargs):
with state.open_scope(*args, **kwargs):
self.__parser._parse(state)
def __imod__(self, other):
self.parser = other
return self
def __call__(self, *args, **kwargs):
return RuleCall(self, *args, **kwargs)
class RuleCall(parser.Unary):
def __init__(self, rule, *args, **kwargs):
if not isinstance(rule, Rule):
raise TypeError('Expected rule to be type Rule, was {}'.format(type(rule).__name__))
super(RuleCall, self).__init__(rule)
self.__args = args
self.__kwargs = kwargs
@property
def args(self):
return self.__args
@property
def kwargs(self):
return dict(self.__kwargs)
def _parse(self, state):
args = [state.invoke(a) for a in self.__args]
kwargs = {k: state.invoke(v) for k, v in self.__kwargs.items()}
self.parser._parse(state, *args, **kwargs)
<｜fim▁end｜> | if self.__expected_attr_type:
return self.__expected_attr_type
else:
try:
inner_parser = self.__parser
except AttributeError:
raise NotImplementedError
else:
return inner_parser.attr_type |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
from . import parser
class Rule(parser.Parser):
def __init__(self, expected_attr_type=None):
self.__expected_attr_type = expected_attr_type
@property
def attr_type(self):
if self.__expected_attr_type:
return self.__expected_attr_type
else:
try:
inner_parser = self.__parser
except AttributeError:
raise NotImplementedError
else:
return inner_parser.attr_type
@property
def parser(self):
<|fim_middle|>
@parser.setter
def parser(self, value):
if self.__expected_attr_type and self.__expected_attr_type != value.attr_type:
raise ValueError('Unexpected attribute type')
self.__parser = parser.as_parser(value)
def _parse(self, state, *args, **kwargs):
with state.open_scope(*args, **kwargs):
self.__parser._parse(state)
def __imod__(self, other):
self.parser = other
return self
def __call__(self, *args, **kwargs):
return RuleCall(self, *args, **kwargs)
class RuleCall(parser.Unary):
def __init__(self, rule, *args, **kwargs):
if not isinstance(rule, Rule):
raise TypeError('Expected rule to be type Rule, was {}'.format(type(rule).__name__))
super(RuleCall, self).__init__(rule)
self.__args = args
self.__kwargs = kwargs
@property
def args(self):
return self.__args
@property
def kwargs(self):
return dict(self.__kwargs)
def _parse(self, state):
args = [state.invoke(a) for a in self.__args]
kwargs = {k: state.invoke(v) for k, v in self.__kwargs.items()}
self.parser._parse(state, *args, **kwargs)
<｜fim▁end｜> | return self.__parser |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
from . import parser
class Rule(parser.Parser):
def __init__(self, expected_attr_type=None):
self.__expected_attr_type = expected_attr_type
@property
def attr_type(self):
if self.__expected_attr_type:
return self.__expected_attr_type
else:
try:
inner_parser = self.__parser
except AttributeError:
raise NotImplementedError
else:
return inner_parser.attr_type
@property
def parser(self):
return self.__parser
@parser.setter
def parser(self, value):
<|fim_middle|>
def _parse(self, state, *args, **kwargs):
with state.open_scope(*args, **kwargs):
self.__parser._parse(state)
def __imod__(self, other):
self.parser = other
return self
def __call__(self, *args, **kwargs):
return RuleCall(self, *args, **kwargs)
class RuleCall(parser.Unary):
def __init__(self, rule, *args, **kwargs):
if not isinstance(rule, Rule):
raise TypeError('Expected rule to be type Rule, was {}'.format(type(rule).__name__))
super(RuleCall, self).__init__(rule)
self.__args = args
self.__kwargs = kwargs
@property
def args(self):
return self.__args
@property
def kwargs(self):
return dict(self.__kwargs)
def _parse(self, state):
args = [state.invoke(a) for a in self.__args]
kwargs = {k: state.invoke(v) for k, v in self.__kwargs.items()}
self.parser._parse(state, *args, **kwargs)
<｜fim▁end｜> | if self.__expected_attr_type and self.__expected_attr_type != value.attr_type:
raise ValueError('Unexpected attribute type')
self.__parser = parser.as_parser(value) |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
from . import parser
class Rule(parser.Parser):
def __init__(self, expected_attr_type=None):
self.__expected_attr_type = expected_attr_type
@property
def attr_type(self):
if self.__expected_attr_type:
return self.__expected_attr_type
else:
try:
inner_parser = self.__parser
except AttributeError:
raise NotImplementedError
else:
return inner_parser.attr_type
@property
def parser(self):
return self.__parser
@parser.setter
def parser(self, value):
if self.__expected_attr_type and self.__expected_attr_type != value.attr_type:
raise ValueError('Unexpected attribute type')
self.__parser = parser.as_parser(value)
def _parse(self, state, *args, **kwargs):
<|fim_middle|>
def __imod__(self, other):
self.parser = other
return self
def __call__(self, *args, **kwargs):
return RuleCall(self, *args, **kwargs)
class RuleCall(parser.Unary):
def __init__(self, rule, *args, **kwargs):
if not isinstance(rule, Rule):
raise TypeError('Expected rule to be type Rule, was {}'.format(type(rule).__name__))
super(RuleCall, self).__init__(rule)
self.__args = args
self.__kwargs = kwargs
@property
def args(self):
return self.__args
@property
def kwargs(self):
return dict(self.__kwargs)
def _parse(self, state):
args = [state.invoke(a) for a in self.__args]
kwargs = {k: state.invoke(v) for k, v in self.__kwargs.items()}
self.parser._parse(state, *args, **kwargs)
<｜fim▁end｜> | with state.open_scope(*args, **kwargs):
self.__parser._parse(state) |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
from . import parser
class Rule(parser.Parser):
def __init__(self, expected_attr_type=None):
self.__expected_attr_type = expected_attr_type
@property
def attr_type(self):
if self.__expected_attr_type:
return self.__expected_attr_type
else:
try:
inner_parser = self.__parser
except AttributeError:
raise NotImplementedError
else:
return inner_parser.attr_type
@property
def parser(self):
return self.__parser
@parser.setter
def parser(self, value):
if self.__expected_attr_type and self.__expected_attr_type != value.attr_type:
raise ValueError('Unexpected attribute type')
self.__parser = parser.as_parser(value)
def _parse(self, state, *args, **kwargs):
with state.open_scope(*args, **kwargs):
self.__parser._parse(state)
def __imod__(self, other):
<|fim_middle|>
def __call__(self, *args, **kwargs):
return RuleCall(self, *args, **kwargs)
class RuleCall(parser.Unary):
def __init__(self, rule, *args, **kwargs):
if not isinstance(rule, Rule):
raise TypeError('Expected rule to be type Rule, was {}'.format(type(rule).__name__))
super(RuleCall, self).__init__(rule)
self.__args = args
self.__kwargs = kwargs
@property
def args(self):
return self.__args
@property
def kwargs(self):
return dict(self.__kwargs)
def _parse(self, state):
args = [state.invoke(a) for a in self.__args]
kwargs = {k: state.invoke(v) for k, v in self.__kwargs.items()}
self.parser._parse(state, *args, **kwargs)
<｜fim▁end｜> | self.parser = other
return self |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
from . import parser
class Rule(parser.Parser):
def __init__(self, expected_attr_type=None):
self.__expected_attr_type = expected_attr_type
@property
def attr_type(self):
if self.__expected_attr_type:
return self.__expected_attr_type
else:
try:
inner_parser = self.__parser
except AttributeError:
raise NotImplementedError
else:
return inner_parser.attr_type
@property
def parser(self):
return self.__parser
@parser.setter
def parser(self, value):
if self.__expected_attr_type and self.__expected_attr_type != value.attr_type:
raise ValueError('Unexpected attribute type')
self.__parser = parser.as_parser(value)
def _parse(self, state, *args, **kwargs):
with state.open_scope(*args, **kwargs):
self.__parser._parse(state)
def __imod__(self, other):
self.parser = other
return self
def __call__(self, *args, **kwargs):
<|fim_middle|>
class RuleCall(parser.Unary):
def __init__(self, rule, *args, **kwargs):
if not isinstance(rule, Rule):
raise TypeError('Expected rule to be type Rule, was {}'.format(type(rule).__name__))
super(RuleCall, self).__init__(rule)
self.__args = args
self.__kwargs = kwargs
@property
def args(self):
return self.__args
@property
def kwargs(self):
return dict(self.__kwargs)
def _parse(self, state):
args = [state.invoke(a) for a in self.__args]
kwargs = {k: state.invoke(v) for k, v in self.__kwargs.items()}
self.parser._parse(state, *args, **kwargs)
<｜fim▁end｜> | return RuleCall(self, *args, **kwargs) |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
from . import parser
class Rule(parser.Parser):
def __init__(self, expected_attr_type=None):
self.__expected_attr_type = expected_attr_type
@property
def attr_type(self):
if self.__expected_attr_type:
return self.__expected_attr_type
else:
try:
inner_parser = self.__parser
except AttributeError:
raise NotImplementedError
else:
return inner_parser.attr_type
@property
def parser(self):
return self.__parser
@parser.setter
def parser(self, value):
if self.__expected_attr_type and self.__expected_attr_type != value.attr_type:
raise ValueError('Unexpected attribute type')
self.__parser = parser.as_parser(value)
def _parse(self, state, *args, **kwargs):
with state.open_scope(*args, **kwargs):
self.__parser._parse(state)
def __imod__(self, other):
self.parser = other
return self
def __call__(self, *args, **kwargs):
return RuleCall(self, *args, **kwargs)
class RuleCall(parser.Unary):
<|fim_middle|>
<｜fim▁end｜> | def __init__(self, rule, *args, **kwargs):
if not isinstance(rule, Rule):
raise TypeError('Expected rule to be type Rule, was {}'.format(type(rule).__name__))
super(RuleCall, self).__init__(rule)
self.__args = args
self.__kwargs = kwargs
@property
def args(self):
return self.__args
@property
def kwargs(self):
return dict(self.__kwargs)
def _parse(self, state):
args = [state.invoke(a) for a in self.__args]
kwargs = {k: state.invoke(v) for k, v in self.__kwargs.items()}
self.parser._parse(state, *args, **kwargs) |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
from . import parser
class Rule(parser.Parser):
def __init__(self, expected_attr_type=None):
self.__expected_attr_type = expected_attr_type
@property
def attr_type(self):
if self.__expected_attr_type:
return self.__expected_attr_type
else:
try:
inner_parser = self.__parser
except AttributeError:
raise NotImplementedError
else:
return inner_parser.attr_type
@property
def parser(self):
return self.__parser
@parser.setter
def parser(self, value):
if self.__expected_attr_type and self.__expected_attr_type != value.attr_type:
raise ValueError('Unexpected attribute type')
self.__parser = parser.as_parser(value)
def _parse(self, state, *args, **kwargs):
with state.open_scope(*args, **kwargs):
self.__parser._parse(state)
def __imod__(self, other):
self.parser = other
return self
def __call__(self, *args, **kwargs):
return RuleCall(self, *args, **kwargs)
class RuleCall(parser.Unary):
def __init__(self, rule, *args, **kwargs):
<|fim_middle|>
@property
def args(self):
return self.__args
@property
def kwargs(self):
return dict(self.__kwargs)
def _parse(self, state):
args = [state.invoke(a) for a in self.__args]
kwargs = {k: state.invoke(v) for k, v in self.__kwargs.items()}
self.parser._parse(state, *args, **kwargs)
<｜fim▁end｜> | if not isinstance(rule, Rule):
raise TypeError('Expected rule to be type Rule, was {}'.format(type(rule).__name__))
super(RuleCall, self).__init__(rule)
self.__args = args
self.__kwargs = kwargs |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
from . import parser
class Rule(parser.Parser):
def __init__(self, expected_attr_type=None):
self.__expected_attr_type = expected_attr_type
@property
def attr_type(self):
if self.__expected_attr_type:
return self.__expected_attr_type
else:
try:
inner_parser = self.__parser
except AttributeError:
raise NotImplementedError
else:
return inner_parser.attr_type
@property
def parser(self):
return self.__parser
@parser.setter
def parser(self, value):
if self.__expected_attr_type and self.__expected_attr_type != value.attr_type:
raise ValueError('Unexpected attribute type')
self.__parser = parser.as_parser(value)
def _parse(self, state, *args, **kwargs):
with state.open_scope(*args, **kwargs):
self.__parser._parse(state)
def __imod__(self, other):
self.parser = other
return self
def __call__(self, *args, **kwargs):
return RuleCall(self, *args, **kwargs)
class RuleCall(parser.Unary):
def __init__(self, rule, *args, **kwargs):
if not isinstance(rule, Rule):
raise TypeError('Expected rule to be type Rule, was {}'.format(type(rule).__name__))
super(RuleCall, self).__init__(rule)
self.__args = args
self.__kwargs = kwargs
@property
def args(self):
<|fim_middle|>
@property
def kwargs(self):
return dict(self.__kwargs)
def _parse(self, state):
args = [state.invoke(a) for a in self.__args]
kwargs = {k: state.invoke(v) for k, v in self.__kwargs.items()}
self.parser._parse(state, *args, **kwargs)
<｜fim▁end｜> | return self.__args |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
from . import parser
class Rule(parser.Parser):
def __init__(self, expected_attr_type=None):
self.__expected_attr_type = expected_attr_type
@property
def attr_type(self):
if self.__expected_attr_type:
return self.__expected_attr_type
else:
try:
inner_parser = self.__parser
except AttributeError:
raise NotImplementedError
else:
return inner_parser.attr_type
@property
def parser(self):
return self.__parser
@parser.setter
def parser(self, value):
if self.__expected_attr_type and self.__expected_attr_type != value.attr_type:
raise ValueError('Unexpected attribute type')
self.__parser = parser.as_parser(value)
def _parse(self, state, *args, **kwargs):
with state.open_scope(*args, **kwargs):
self.__parser._parse(state)
def __imod__(self, other):
self.parser = other
return self
def __call__(self, *args, **kwargs):
return RuleCall(self, *args, **kwargs)
class RuleCall(parser.Unary):
def __init__(self, rule, *args, **kwargs):
if not isinstance(rule, Rule):
raise TypeError('Expected rule to be type Rule, was {}'.format(type(rule).__name__))
super(RuleCall, self).__init__(rule)
self.__args = args
self.__kwargs = kwargs
@property
def args(self):
return self.__args
@property
def kwargs(self):
<|fim_middle|>
def _parse(self, state):
args = [state.invoke(a) for a in self.__args]
kwargs = {k: state.invoke(v) for k, v in self.__kwargs.items()}
self.parser._parse(state, *args, **kwargs)
<｜fim▁end｜> | return dict(self.__kwargs) |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
from . import parser
class Rule(parser.Parser):
def __init__(self, expected_attr_type=None):
self.__expected_attr_type = expected_attr_type
@property
def attr_type(self):
if self.__expected_attr_type:
return self.__expected_attr_type
else:
try:
inner_parser = self.__parser
except AttributeError:
raise NotImplementedError
else:
return inner_parser.attr_type
@property
def parser(self):
return self.__parser
@parser.setter
def parser(self, value):
if self.__expected_attr_type and self.__expected_attr_type != value.attr_type:
raise ValueError('Unexpected attribute type')
self.__parser = parser.as_parser(value)
def _parse(self, state, *args, **kwargs):
with state.open_scope(*args, **kwargs):
self.__parser._parse(state)
def __imod__(self, other):
self.parser = other
return self
def __call__(self, *args, **kwargs):
return RuleCall(self, *args, **kwargs)
class RuleCall(parser.Unary):
def __init__(self, rule, *args, **kwargs):
if not isinstance(rule, Rule):
raise TypeError('Expected rule to be type Rule, was {}'.format(type(rule).__name__))
super(RuleCall, self).__init__(rule)
self.__args = args
self.__kwargs = kwargs
@property
def args(self):
return self.__args
@property
def kwargs(self):
return dict(self.__kwargs)
def _parse(self, state):
<|fim_middle|>
<｜fim▁end｜> | args = [state.invoke(a) for a in self.__args]
kwargs = {k: state.invoke(v) for k, v in self.__kwargs.items()}
self.parser._parse(state, *args, **kwargs) |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
from . import parser
class Rule(parser.Parser):
def __init__(self, expected_attr_type=None):
self.__expected_attr_type = expected_attr_type
@property
def attr_type(self):
if self.__expected_attr_type:
<|fim_middle|>
else:
try:
inner_parser = self.__parser
except AttributeError:
raise NotImplementedError
else:
return inner_parser.attr_type
@property
def parser(self):
return self.__parser
@parser.setter
def parser(self, value):
if self.__expected_attr_type and self.__expected_attr_type != value.attr_type:
raise ValueError('Unexpected attribute type')
self.__parser = parser.as_parser(value)
def _parse(self, state, *args, **kwargs):
with state.open_scope(*args, **kwargs):
self.__parser._parse(state)
def __imod__(self, other):
self.parser = other
return self
def __call__(self, *args, **kwargs):
return RuleCall(self, *args, **kwargs)
class RuleCall(parser.Unary):
def __init__(self, rule, *args, **kwargs):
if not isinstance(rule, Rule):
raise TypeError('Expected rule to be type Rule, was {}'.format(type(rule).__name__))
super(RuleCall, self).__init__(rule)
self.__args = args
self.__kwargs = kwargs
@property
def args(self):
return self.__args
@property
def kwargs(self):
return dict(self.__kwargs)
def _parse(self, state):
args = [state.invoke(a) for a in self.__args]
kwargs = {k: state.invoke(v) for k, v in self.__kwargs.items()}
self.parser._parse(state, *args, **kwargs)
<｜fim▁end｜> | return self.__expected_attr_type |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
from . import parser
class Rule(parser.Parser):
def __init__(self, expected_attr_type=None):
self.__expected_attr_type = expected_attr_type
@property
def attr_type(self):
if self.__expected_attr_type:
return self.__expected_attr_type
else:
<|fim_middle|>
@property
def parser(self):
return self.__parser
@parser.setter
def parser(self, value):
if self.__expected_attr_type and self.__expected_attr_type != value.attr_type:
raise ValueError('Unexpected attribute type')
self.__parser = parser.as_parser(value)
def _parse(self, state, *args, **kwargs):
with state.open_scope(*args, **kwargs):
self.__parser._parse(state)
def __imod__(self, other):
self.parser = other
return self
def __call__(self, *args, **kwargs):
return RuleCall(self, *args, **kwargs)
class RuleCall(parser.Unary):
def __init__(self, rule, *args, **kwargs):
if not isinstance(rule, Rule):
raise TypeError('Expected rule to be type Rule, was {}'.format(type(rule).__name__))
super(RuleCall, self).__init__(rule)
self.__args = args
self.__kwargs = kwargs
@property
def args(self):
return self.__args
@property
def kwargs(self):
return dict(self.__kwargs)
def _parse(self, state):
args = [state.invoke(a) for a in self.__args]
kwargs = {k: state.invoke(v) for k, v in self.__kwargs.items()}
self.parser._parse(state, *args, **kwargs)
<｜fim▁end｜> | try:
inner_parser = self.__parser
except AttributeError:
raise NotImplementedError
else:
return inner_parser.attr_type |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
from . import parser
class Rule(parser.Parser):
def __init__(self, expected_attr_type=None):
self.__expected_attr_type = expected_attr_type
@property
def attr_type(self):
if self.__expected_attr_type:
return self.__expected_attr_type
else:
try:
inner_parser = self.__parser
except AttributeError:
raise NotImplementedError
else:
<|fim_middle|>
@property
def parser(self):
return self.__parser
@parser.setter
def parser(self, value):
if self.__expected_attr_type and self.__expected_attr_type != value.attr_type:
raise ValueError('Unexpected attribute type')
self.__parser = parser.as_parser(value)
def _parse(self, state, *args, **kwargs):
with state.open_scope(*args, **kwargs):
self.__parser._parse(state)
def __imod__(self, other):
self.parser = other
return self
def __call__(self, *args, **kwargs):
return RuleCall(self, *args, **kwargs)
class RuleCall(parser.Unary):
def __init__(self, rule, *args, **kwargs):
if not isinstance(rule, Rule):
raise TypeError('Expected rule to be type Rule, was {}'.format(type(rule).__name__))
super(RuleCall, self).__init__(rule)
self.__args = args
self.__kwargs = kwargs
@property
def args(self):
return self.__args
@property
def kwargs(self):
return dict(self.__kwargs)
def _parse(self, state):
args = [state.invoke(a) for a in self.__args]
kwargs = {k: state.invoke(v) for k, v in self.__kwargs.items()}
self.parser._parse(state, *args, **kwargs)
<｜fim▁end｜> | return inner_parser.attr_type |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
from . import parser
class Rule(parser.Parser):
def __init__(self, expected_attr_type=None):
self.__expected_attr_type = expected_attr_type
@property
def attr_type(self):
if self.__expected_attr_type:
return self.__expected_attr_type
else:
try:
inner_parser = self.__parser
except AttributeError:
raise NotImplementedError
else:
return inner_parser.attr_type
@property
def parser(self):
return self.__parser
@parser.setter
def parser(self, value):
if self.__expected_attr_type and self.__expected_attr_type != value.attr_type:
<|fim_middle|>
self.__parser = parser.as_parser(value)
def _parse(self, state, *args, **kwargs):
with state.open_scope(*args, **kwargs):
self.__parser._parse(state)
def __imod__(self, other):
self.parser = other
return self
def __call__(self, *args, **kwargs):
return RuleCall(self, *args, **kwargs)
class RuleCall(parser.Unary):
def __init__(self, rule, *args, **kwargs):
if not isinstance(rule, Rule):
raise TypeError('Expected rule to be type Rule, was {}'.format(type(rule).__name__))
super(RuleCall, self).__init__(rule)
self.__args = args
self.__kwargs = kwargs
@property
def args(self):
return self.__args
@property
def kwargs(self):
return dict(self.__kwargs)
def _parse(self, state):
args = [state.invoke(a) for a in self.__args]
kwargs = {k: state.invoke(v) for k, v in self.__kwargs.items()}
self.parser._parse(state, *args, **kwargs)
<｜fim▁end｜> | raise ValueError('Unexpected attribute type') |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
from . import parser
class Rule(parser.Parser):
def __init__(self, expected_attr_type=None):
self.__expected_attr_type = expected_attr_type
@property
def attr_type(self):
if self.__expected_attr_type:
return self.__expected_attr_type
else:
try:
inner_parser = self.__parser
except AttributeError:
raise NotImplementedError
else:
return inner_parser.attr_type
@property
def parser(self):
return self.__parser
@parser.setter
def parser(self, value):
if self.__expected_attr_type and self.__expected_attr_type != value.attr_type:
raise ValueError('Unexpected attribute type')
self.__parser = parser.as_parser(value)
def _parse(self, state, *args, **kwargs):
with state.open_scope(*args, **kwargs):
self.__parser._parse(state)
def __imod__(self, other):
self.parser = other
return self
def __call__(self, *args, **kwargs):
return RuleCall(self, *args, **kwargs)
class RuleCall(parser.Unary):
def __init__(self, rule, *args, **kwargs):
if not isinstance(rule, Rule):
<|fim_middle|>
super(RuleCall, self).__init__(rule)
self.__args = args
self.__kwargs = kwargs
@property
def args(self):
return self.__args
@property
def kwargs(self):
return dict(self.__kwargs)
def _parse(self, state):
args = [state.invoke(a) for a in self.__args]
kwargs = {k: state.invoke(v) for k, v in self.__kwargs.items()}
self.parser._parse(state, *args, **kwargs)
<｜fim▁end｜> | raise TypeError('Expected rule to be type Rule, was {}'.format(type(rule).__name__)) |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
from . import parser
class Rule(parser.Parser):
def <|fim_middle|>(self, expected_attr_type=None):
self.__expected_attr_type = expected_attr_type
@property
def attr_type(self):
if self.__expected_attr_type:
return self.__expected_attr_type
else:
try:
inner_parser = self.__parser
except AttributeError:
raise NotImplementedError
else:
return inner_parser.attr_type
@property
def parser(self):
return self.__parser
@parser.setter
def parser(self, value):
if self.__expected_attr_type and self.__expected_attr_type != value.attr_type:
raise ValueError('Unexpected attribute type')
self.__parser = parser.as_parser(value)
def _parse(self, state, *args, **kwargs):
with state.open_scope(*args, **kwargs):
self.__parser._parse(state)
def __imod__(self, other):
self.parser = other
return self
def __call__(self, *args, **kwargs):
return RuleCall(self, *args, **kwargs)
class RuleCall(parser.Unary):
def __init__(self, rule, *args, **kwargs):
if not isinstance(rule, Rule):
raise TypeError('Expected rule to be type Rule, was {}'.format(type(rule).__name__))
super(RuleCall, self).__init__(rule)
self.__args = args
self.__kwargs = kwargs
@property
def args(self):
return self.__args
@property
def kwargs(self):
return dict(self.__kwargs)
def _parse(self, state):
args = [state.invoke(a) for a in self.__args]
kwargs = {k: state.invoke(v) for k, v in self.__kwargs.items()}
self.parser._parse(state, *args, **kwargs)
<｜fim▁end｜> | __init__ |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
from . import parser
class Rule(parser.Parser):
def __init__(self, expected_attr_type=None):
self.__expected_attr_type = expected_attr_type
@property
def <|fim_middle|>(self):
if self.__expected_attr_type:
return self.__expected_attr_type
else:
try:
inner_parser = self.__parser
except AttributeError:
raise NotImplementedError
else:
return inner_parser.attr_type
@property
def parser(self):
return self.__parser
@parser.setter
def parser(self, value):
if self.__expected_attr_type and self.__expected_attr_type != value.attr_type:
raise ValueError('Unexpected attribute type')
self.__parser = parser.as_parser(value)
def _parse(self, state, *args, **kwargs):
with state.open_scope(*args, **kwargs):
self.__parser._parse(state)
def __imod__(self, other):
self.parser = other
return self
def __call__(self, *args, **kwargs):
return RuleCall(self, *args, **kwargs)
class RuleCall(parser.Unary):
def __init__(self, rule, *args, **kwargs):
if not isinstance(rule, Rule):
raise TypeError('Expected rule to be type Rule, was {}'.format(type(rule).__name__))
super(RuleCall, self).__init__(rule)
self.__args = args
self.__kwargs = kwargs
@property
def args(self):
return self.__args
@property
def kwargs(self):
return dict(self.__kwargs)
def _parse(self, state):
args = [state.invoke(a) for a in self.__args]
kwargs = {k: state.invoke(v) for k, v in self.__kwargs.items()}
self.parser._parse(state, *args, **kwargs)
<｜fim▁end｜> | attr_type |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
from . import parser
class Rule(parser.Parser):
def __init__(self, expected_attr_type=None):
self.__expected_attr_type = expected_attr_type
@property
def attr_type(self):
if self.__expected_attr_type:
return self.__expected_attr_type
else:
try:
inner_parser = self.__parser
except AttributeError:
raise NotImplementedError
else:
return inner_parser.attr_type
@property
def <|fim_middle|>(self):
return self.__parser
@parser.setter
def parser(self, value):
if self.__expected_attr_type and self.__expected_attr_type != value.attr_type:
raise ValueError('Unexpected attribute type')
self.__parser = parser.as_parser(value)
def _parse(self, state, *args, **kwargs):
with state.open_scope(*args, **kwargs):
self.__parser._parse(state)
def __imod__(self, other):
self.parser = other
return self
def __call__(self, *args, **kwargs):
return RuleCall(self, *args, **kwargs)
class RuleCall(parser.Unary):
def __init__(self, rule, *args, **kwargs):
if not isinstance(rule, Rule):
raise TypeError('Expected rule to be type Rule, was {}'.format(type(rule).__name__))
super(RuleCall, self).__init__(rule)
self.__args = args
self.__kwargs = kwargs
@property
def args(self):
return self.__args
@property
def kwargs(self):
return dict(self.__kwargs)
def _parse(self, state):
args = [state.invoke(a) for a in self.__args]
kwargs = {k: state.invoke(v) for k, v in self.__kwargs.items()}
self.parser._parse(state, *args, **kwargs)
<｜fim▁end｜> | parser |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
from . import parser
class Rule(parser.Parser):
def __init__(self, expected_attr_type=None):
self.__expected_attr_type = expected_attr_type
@property
def attr_type(self):
if self.__expected_attr_type:
return self.__expected_attr_type
else:
try:
inner_parser = self.__parser
except AttributeError:
raise NotImplementedError
else:
return inner_parser.attr_type
@property
def parser(self):
return self.__parser
@parser.setter
def <|fim_middle|>(self, value):
if self.__expected_attr_type and self.__expected_attr_type != value.attr_type:
raise ValueError('Unexpected attribute type')
self.__parser = parser.as_parser(value)
def _parse(self, state, *args, **kwargs):
with state.open_scope(*args, **kwargs):
self.__parser._parse(state)
def __imod__(self, other):
self.parser = other
return self
def __call__(self, *args, **kwargs):
return RuleCall(self, *args, **kwargs)
class RuleCall(parser.Unary):
def __init__(self, rule, *args, **kwargs):
if not isinstance(rule, Rule):
raise TypeError('Expected rule to be type Rule, was {}'.format(type(rule).__name__))
super(RuleCall, self).__init__(rule)
self.__args = args
self.__kwargs = kwargs
@property
def args(self):
return self.__args
@property
def kwargs(self):
return dict(self.__kwargs)
def _parse(self, state):
args = [state.invoke(a) for a in self.__args]
kwargs = {k: state.invoke(v) for k, v in self.__kwargs.items()}
self.parser._parse(state, *args, **kwargs)
<｜fim▁end｜> | parser |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
from . import parser
class Rule(parser.Parser):
def __init__(self, expected_attr_type=None):
self.__expected_attr_type = expected_attr_type
@property
def attr_type(self):
if self.__expected_attr_type:
return self.__expected_attr_type
else:
try:
inner_parser = self.__parser
except AttributeError:
raise NotImplementedError
else:
return inner_parser.attr_type
@property
def parser(self):
return self.__parser
@parser.setter
def parser(self, value):
if self.__expected_attr_type and self.__expected_attr_type != value.attr_type:
raise ValueError('Unexpected attribute type')
self.__parser = parser.as_parser(value)
def <|fim_middle|>(self, state, *args, **kwargs):
with state.open_scope(*args, **kwargs):
self.__parser._parse(state)
def __imod__(self, other):
self.parser = other
return self
def __call__(self, *args, **kwargs):
return RuleCall(self, *args, **kwargs)
class RuleCall(parser.Unary):
def __init__(self, rule, *args, **kwargs):
if not isinstance(rule, Rule):
raise TypeError('Expected rule to be type Rule, was {}'.format(type(rule).__name__))
super(RuleCall, self).__init__(rule)
self.__args = args
self.__kwargs = kwargs
@property
def args(self):
return self.__args
@property
def kwargs(self):
return dict(self.__kwargs)
def _parse(self, state):
args = [state.invoke(a) for a in self.__args]
kwargs = {k: state.invoke(v) for k, v in self.__kwargs.items()}
self.parser._parse(state, *args, **kwargs)
<｜fim▁end｜> | _parse |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
from . import parser
class Rule(parser.Parser):
def __init__(self, expected_attr_type=None):
self.__expected_attr_type = expected_attr_type
@property
def attr_type(self):
if self.__expected_attr_type:
return self.__expected_attr_type
else:
try:
inner_parser = self.__parser
except AttributeError:
raise NotImplementedError
else:
return inner_parser.attr_type
@property
def parser(self):
return self.__parser
@parser.setter
def parser(self, value):
if self.__expected_attr_type and self.__expected_attr_type != value.attr_type:
raise ValueError('Unexpected attribute type')
self.__parser = parser.as_parser(value)
def _parse(self, state, *args, **kwargs):
with state.open_scope(*args, **kwargs):
self.__parser._parse(state)
def <|fim_middle|>(self, other):
self.parser = other
return self
def __call__(self, *args, **kwargs):
return RuleCall(self, *args, **kwargs)
class RuleCall(parser.Unary):
def __init__(self, rule, *args, **kwargs):
if not isinstance(rule, Rule):
raise TypeError('Expected rule to be type Rule, was {}'.format(type(rule).__name__))
super(RuleCall, self).__init__(rule)
self.__args = args
self.__kwargs = kwargs
@property
def args(self):
return self.__args
@property
def kwargs(self):
return dict(self.__kwargs)
def _parse(self, state):
args = [state.invoke(a) for a in self.__args]
kwargs = {k: state.invoke(v) for k, v in self.__kwargs.items()}
self.parser._parse(state, *args, **kwargs)
<｜fim▁end｜> | __imod__ |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
from . import parser
class Rule(parser.Parser):
def __init__(self, expected_attr_type=None):
self.__expected_attr_type = expected_attr_type
@property
def attr_type(self):
if self.__expected_attr_type:
return self.__expected_attr_type
else:
try:
inner_parser = self.__parser
except AttributeError:
raise NotImplementedError
else:
return inner_parser.attr_type
@property
def parser(self):
return self.__parser
@parser.setter
def parser(self, value):
if self.__expected_attr_type and self.__expected_attr_type != value.attr_type:
raise ValueError('Unexpected attribute type')
self.__parser = parser.as_parser(value)
def _parse(self, state, *args, **kwargs):
with state.open_scope(*args, **kwargs):
self.__parser._parse(state)
def __imod__(self, other):
self.parser = other
return self
def <|fim_middle|>(self, *args, **kwargs):
return RuleCall(self, *args, **kwargs)
class RuleCall(parser.Unary):
def __init__(self, rule, *args, **kwargs):
if not isinstance(rule, Rule):
raise TypeError('Expected rule to be type Rule, was {}'.format(type(rule).__name__))
super(RuleCall, self).__init__(rule)
self.__args = args
self.__kwargs = kwargs
@property
def args(self):
return self.__args
@property
def kwargs(self):
return dict(self.__kwargs)
def _parse(self, state):
args = [state.invoke(a) for a in self.__args]
kwargs = {k: state.invoke(v) for k, v in self.__kwargs.items()}
self.parser._parse(state, *args, **kwargs)
<｜fim▁end｜> | __call__ |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
from . import parser
class Rule(parser.Parser):
def __init__(self, expected_attr_type=None):
self.__expected_attr_type = expected_attr_type
@property
def attr_type(self):
if self.__expected_attr_type:
return self.__expected_attr_type
else:
try:
inner_parser = self.__parser
except AttributeError:
raise NotImplementedError
else:
return inner_parser.attr_type
@property
def parser(self):
return self.__parser
@parser.setter
def parser(self, value):
if self.__expected_attr_type and self.__expected_attr_type != value.attr_type:
raise ValueError('Unexpected attribute type')
self.__parser = parser.as_parser(value)
def _parse(self, state, *args, **kwargs):
with state.open_scope(*args, **kwargs):
self.__parser._parse(state)
def __imod__(self, other):
self.parser = other
return self
def __call__(self, *args, **kwargs):
return RuleCall(self, *args, **kwargs)
class RuleCall(parser.Unary):
def <|fim_middle|>(self, rule, *args, **kwargs):
if not isinstance(rule, Rule):
raise TypeError('Expected rule to be type Rule, was {}'.format(type(rule).__name__))
super(RuleCall, self).__init__(rule)
self.__args = args
self.__kwargs = kwargs
@property
def args(self):
return self.__args
@property
def kwargs(self):
return dict(self.__kwargs)
def _parse(self, state):
args = [state.invoke(a) for a in self.__args]
kwargs = {k: state.invoke(v) for k, v in self.__kwargs.items()}
self.parser._parse(state, *args, **kwargs)
<｜fim▁end｜> | __init__ |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
from . import parser
class Rule(parser.Parser):
def __init__(self, expected_attr_type=None):
self.__expected_attr_type = expected_attr_type
@property
def attr_type(self):
if self.__expected_attr_type:
return self.__expected_attr_type
else:
try:
inner_parser = self.__parser
except AttributeError:
raise NotImplementedError
else:
return inner_parser.attr_type
@property
def parser(self):
return self.__parser
@parser.setter
def parser(self, value):
if self.__expected_attr_type and self.__expected_attr_type != value.attr_type:
raise ValueError('Unexpected attribute type')
self.__parser = parser.as_parser(value)
def _parse(self, state, *args, **kwargs):
with state.open_scope(*args, **kwargs):
self.__parser._parse(state)
def __imod__(self, other):
self.parser = other
return self
def __call__(self, *args, **kwargs):
return RuleCall(self, *args, **kwargs)
class RuleCall(parser.Unary):
def __init__(self, rule, *args, **kwargs):
if not isinstance(rule, Rule):
raise TypeError('Expected rule to be type Rule, was {}'.format(type(rule).__name__))
super(RuleCall, self).__init__(rule)
self.__args = args
self.__kwargs = kwargs
@property
def <|fim_middle|>(self):
return self.__args
@property
def kwargs(self):
return dict(self.__kwargs)
def _parse(self, state):
args = [state.invoke(a) for a in self.__args]
kwargs = {k: state.invoke(v) for k, v in self.__kwargs.items()}
self.parser._parse(state, *args, **kwargs)
<｜fim▁end｜> | args |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
from . import parser
class Rule(parser.Parser):
def __init__(self, expected_attr_type=None):
self.__expected_attr_type = expected_attr_type
@property
def attr_type(self):
if self.__expected_attr_type:
return self.__expected_attr_type
else:
try:
inner_parser = self.__parser
except AttributeError:
raise NotImplementedError
else:
return inner_parser.attr_type
@property
def parser(self):
return self.__parser
@parser.setter
def parser(self, value):
if self.__expected_attr_type and self.__expected_attr_type != value.attr_type:
raise ValueError('Unexpected attribute type')
self.__parser = parser.as_parser(value)
def _parse(self, state, *args, **kwargs):
with state.open_scope(*args, **kwargs):
self.__parser._parse(state)
def __imod__(self, other):
self.parser = other
return self
def __call__(self, *args, **kwargs):
return RuleCall(self, *args, **kwargs)
class RuleCall(parser.Unary):
def __init__(self, rule, *args, **kwargs):
if not isinstance(rule, Rule):
raise TypeError('Expected rule to be type Rule, was {}'.format(type(rule).__name__))
super(RuleCall, self).__init__(rule)
self.__args = args
self.__kwargs = kwargs
@property
def args(self):
return self.__args
@property
def <|fim_middle|>(self):
return dict(self.__kwargs)
def _parse(self, state):
args = [state.invoke(a) for a in self.__args]
kwargs = {k: state.invoke(v) for k, v in self.__kwargs.items()}
self.parser._parse(state, *args, **kwargs)
<｜fim▁end｜> | kwargs |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
from . import parser
class Rule(parser.Parser):
def __init__(self, expected_attr_type=None):
self.__expected_attr_type = expected_attr_type
@property
def attr_type(self):
if self.__expected_attr_type:
return self.__expected_attr_type
else:
try:
inner_parser = self.__parser
except AttributeError:
raise NotImplementedError
else:
return inner_parser.attr_type
@property
def parser(self):
return self.__parser
@parser.setter
def parser(self, value):
if self.__expected_attr_type and self.__expected_attr_type != value.attr_type:
raise ValueError('Unexpected attribute type')
self.__parser = parser.as_parser(value)
def _parse(self, state, *args, **kwargs):
with state.open_scope(*args, **kwargs):
self.__parser._parse(state)
def __imod__(self, other):
self.parser = other
return self
def __call__(self, *args, **kwargs):
return RuleCall(self, *args, **kwargs)
class RuleCall(parser.Unary):
def __init__(self, rule, *args, **kwargs):
if not isinstance(rule, Rule):
raise TypeError('Expected rule to be type Rule, was {}'.format(type(rule).__name__))
super(RuleCall, self).__init__(rule)
self.__args = args
self.__kwargs = kwargs
@property
def args(self):
return self.__args
@property
def kwargs(self):
return dict(self.__kwargs)
def <|fim_middle|>(self, state):
args = [state.invoke(a) for a in self.__args]
kwargs = {k: state.invoke(v) for k, v in self.__kwargs.items()}
self.parser._parse(state, *args, **kwargs)
<｜fim▁end｜> | _parse |
<|file_name|>models.py<|end_file_name|><｜fim▁begin｜>from django.utils.translation import ugettext as _
from django.db import models
from jmbo.models import ModelBase
<｜fim▁hole｜>
class Superhero(ModelBase):
name = models.CharField(max_length=256, editable=False)
class Meta:
verbose_name_plural = _("Superheroes")<｜fim▁end｜> | |
<|file_name|>models.py<|end_file_name|><｜fim▁begin｜>from django.utils.translation import ugettext as _
from django.db import models
from jmbo.models import ModelBase
class Superhero(ModelBase):
<|fim_middle|>
<｜fim▁end｜> | name = models.CharField(max_length=256, editable=False)
class Meta:
verbose_name_plural = _("Superheroes") |
<|file_name|>models.py<|end_file_name|><｜fim▁begin｜>from django.utils.translation import ugettext as _
from django.db import models
from jmbo.models import ModelBase
class Superhero(ModelBase):
name = models.CharField(max_length=256, editable=False)
class Meta:
<|fim_middle|>
<｜fim▁end｜> | verbose_name_plural = _("Superheroes") |
<|file_name|>pyqt4.py<|end_file_name|><｜fim▁begin｜># -*- coding: utf-8 -*-
# Copyright (C) 2010, 2011, 2012, 2013 Sebastian Wiesner <[email protected]>
# This library is free software; you can redistribute it and/or modify it
# under the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation; either version 2.1 of the License, or (at your
# option) any later version.
# This library is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
# for more details.
# You should have received a copy of the GNU Lesser General Public License
# along with this library; if not, write to the Free Software Foundation,
# Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
# pylint: disable=anomalous-backslash-in-string
"""
pyudev.pyqt4
============
PyQt4 integration.
:class:`MonitorObserver` integrates device monitoring into the PyQt4\_
mainloop by turning device events into Qt signals.
:mod:`PyQt4.QtCore` from PyQt4\_ must be available when importing this
module.
.. _PyQt4: http://riverbankcomputing.co.uk/software/pyqt/intro<｜fim▁hole｜>
from __future__ import (print_function, division, unicode_literals,
absolute_import)
from PyQt4.QtCore import QSocketNotifier, QObject, pyqtSignal
from pyudev._util import text_type
from pyudev.core import Device
from pyudev._qt_base import QUDevMonitorObserverMixin, MonitorObserverMixin
class MonitorObserver(QObject, MonitorObserverMixin):
"""An observer for device events integrating into the :mod:`PyQt4` mainloop.
This class inherits :class:`~PyQt4.QtCore.QObject` to turn device events
into Qt signals:
>>> from pyudev import Context, Monitor
>>> from pyudev.pyqt4 import MonitorObserver
>>> context = Context()
>>> monitor = Monitor.from_netlink(context)
>>> monitor.filter_by(subsystem='input')
>>> observer = MonitorObserver(monitor)
>>> def device_event(device):
... print('event {0} on device {1}'.format(device.action, device))
>>> observer.deviceEvent.connect(device_event)
>>> monitor.start()
This class is a child of :class:`~PyQt4.QtCore.QObject`.
"""
#: emitted upon arbitrary device events
deviceEvent = pyqtSignal(Device)
def __init__(self, monitor, parent=None):
"""
Observe the given ``monitor`` (a :class:`~pyudev.Monitor`):
``parent`` is the parent :class:`~PyQt4.QtCore.QObject` of this
object. It is passed unchanged to the inherited constructor of
:class:`~PyQt4.QtCore.QObject`.
"""
QObject.__init__(self, parent)
self._setup_notifier(monitor, QSocketNotifier)
class QUDevMonitorObserver(QObject, QUDevMonitorObserverMixin):
"""An observer for device events integrating into the :mod:`PyQt4` mainloop.
.. deprecated:: 0.17
Will be removed in 1.0. Use :class:`MonitorObserver` instead.
"""
#: emitted upon arbitrary device events
deviceEvent = pyqtSignal(text_type, Device)
#: emitted, if a device was added
deviceAdded = pyqtSignal(Device)
#: emitted, if a device was removed
deviceRemoved = pyqtSignal(Device)
#: emitted, if a device was changed
deviceChanged = pyqtSignal(Device)
#: emitted, if a device was moved
deviceMoved = pyqtSignal(Device)
def __init__(self, monitor, parent=None):
"""
Observe the given ``monitor`` (a :class:`~pyudev.Monitor`):
``parent`` is the parent :class:`~PyQt4.QtCore.QObject` of this
object. It is passed unchanged to the inherited constructor of
:class:`~PyQt4.QtCore.QObject`.
"""
QObject.__init__(self, parent)
self._setup_notifier(monitor, QSocketNotifier)<｜fim▁end｜> |
.. moduleauthor:: Sebastian Wiesner <[email protected]>
""" |
<|file_name|>pyqt4.py<|end_file_name|><｜fim▁begin｜># -*- coding: utf-8 -*-
# Copyright (C) 2010, 2011, 2012, 2013 Sebastian Wiesner <[email protected]>
# This library is free software; you can redistribute it and/or modify it
# under the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation; either version 2.1 of the License, or (at your
# option) any later version.
# This library is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
# for more details.
# You should have received a copy of the GNU Lesser General Public License
# along with this library; if not, write to the Free Software Foundation,
# Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
# pylint: disable=anomalous-backslash-in-string
"""
pyudev.pyqt4
============
PyQt4 integration.
:class:`MonitorObserver` integrates device monitoring into the PyQt4\_
mainloop by turning device events into Qt signals.
:mod:`PyQt4.QtCore` from PyQt4\_ must be available when importing this
module.
.. _PyQt4: http://riverbankcomputing.co.uk/software/pyqt/intro
.. moduleauthor:: Sebastian Wiesner <[email protected]>
"""
from __future__ import (print_function, division, unicode_literals,
absolute_import)
from PyQt4.QtCore import QSocketNotifier, QObject, pyqtSignal
from pyudev._util import text_type
from pyudev.core import Device
from pyudev._qt_base import QUDevMonitorObserverMixin, MonitorObserverMixin
class MonitorObserver(QObject, MonitorObserverMixin):
<|fim_middle|>
class QUDevMonitorObserver(QObject, QUDevMonitorObserverMixin):
"""An observer for device events integrating into the :mod:`PyQt4` mainloop.
.. deprecated:: 0.17
Will be removed in 1.0. Use :class:`MonitorObserver` instead.
"""
#: emitted upon arbitrary device events
deviceEvent = pyqtSignal(text_type, Device)
#: emitted, if a device was added
deviceAdded = pyqtSignal(Device)
#: emitted, if a device was removed
deviceRemoved = pyqtSignal(Device)
#: emitted, if a device was changed
deviceChanged = pyqtSignal(Device)
#: emitted, if a device was moved
deviceMoved = pyqtSignal(Device)
def __init__(self, monitor, parent=None):
"""
Observe the given ``monitor`` (a :class:`~pyudev.Monitor`):
``parent`` is the parent :class:`~PyQt4.QtCore.QObject` of this
object. It is passed unchanged to the inherited constructor of
:class:`~PyQt4.QtCore.QObject`.
"""
QObject.__init__(self, parent)
self._setup_notifier(monitor, QSocketNotifier)
<｜fim▁end｜> | """An observer for device events integrating into the :mod:`PyQt4` mainloop.
This class inherits :class:`~PyQt4.QtCore.QObject` to turn device events
into Qt signals:
>>> from pyudev import Context, Monitor
>>> from pyudev.pyqt4 import MonitorObserver
>>> context = Context()
>>> monitor = Monitor.from_netlink(context)
>>> monitor.filter_by(subsystem='input')
>>> observer = MonitorObserver(monitor)
>>> def device_event(device):
... print('event {0} on device {1}'.format(device.action, device))
>>> observer.deviceEvent.connect(device_event)
>>> monitor.start()
This class is a child of :class:`~PyQt4.QtCore.QObject`.
"""
#: emitted upon arbitrary device events
deviceEvent = pyqtSignal(Device)
def __init__(self, monitor, parent=None):
"""
Observe the given ``monitor`` (a :class:`~pyudev.Monitor`):
``parent`` is the parent :class:`~PyQt4.QtCore.QObject` of this
object. It is passed unchanged to the inherited constructor of
:class:`~PyQt4.QtCore.QObject`.
"""
QObject.__init__(self, parent)
self._setup_notifier(monitor, QSocketNotifier) |
<|file_name|>pyqt4.py<|end_file_name|><｜fim▁begin｜># -*- coding: utf-8 -*-
# Copyright (C) 2010, 2011, 2012, 2013 Sebastian Wiesner <[email protected]>
# This library is free software; you can redistribute it and/or modify it
# under the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation; either version 2.1 of the License, or (at your
# option) any later version.
# This library is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
# for more details.
# You should have received a copy of the GNU Lesser General Public License
# along with this library; if not, write to the Free Software Foundation,
# Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
# pylint: disable=anomalous-backslash-in-string
"""
pyudev.pyqt4
============
PyQt4 integration.
:class:`MonitorObserver` integrates device monitoring into the PyQt4\_
mainloop by turning device events into Qt signals.
:mod:`PyQt4.QtCore` from PyQt4\_ must be available when importing this
module.
.. _PyQt4: http://riverbankcomputing.co.uk/software/pyqt/intro
.. moduleauthor:: Sebastian Wiesner <[email protected]>
"""
from __future__ import (print_function, division, unicode_literals,
absolute_import)
from PyQt4.QtCore import QSocketNotifier, QObject, pyqtSignal
from pyudev._util import text_type
from pyudev.core import Device
from pyudev._qt_base import QUDevMonitorObserverMixin, MonitorObserverMixin
class MonitorObserver(QObject, MonitorObserverMixin):
"""An observer for device events integrating into the :mod:`PyQt4` mainloop.
This class inherits :class:`~PyQt4.QtCore.QObject` to turn device events
into Qt signals:
>>> from pyudev import Context, Monitor
>>> from pyudev.pyqt4 import MonitorObserver
>>> context = Context()
>>> monitor = Monitor.from_netlink(context)
>>> monitor.filter_by(subsystem='input')
>>> observer = MonitorObserver(monitor)
>>> def device_event(device):
... print('event {0} on device {1}'.format(device.action, device))
>>> observer.deviceEvent.connect(device_event)
>>> monitor.start()
This class is a child of :class:`~PyQt4.QtCore.QObject`.
"""
#: emitted upon arbitrary device events
deviceEvent = pyqtSignal(Device)
def __init__(self, monitor, parent=None):
<|fim_middle|>
class QUDevMonitorObserver(QObject, QUDevMonitorObserverMixin):
"""An observer for device events integrating into the :mod:`PyQt4` mainloop.
.. deprecated:: 0.17
Will be removed in 1.0. Use :class:`MonitorObserver` instead.
"""
#: emitted upon arbitrary device events
deviceEvent = pyqtSignal(text_type, Device)
#: emitted, if a device was added
deviceAdded = pyqtSignal(Device)
#: emitted, if a device was removed
deviceRemoved = pyqtSignal(Device)
#: emitted, if a device was changed
deviceChanged = pyqtSignal(Device)
#: emitted, if a device was moved
deviceMoved = pyqtSignal(Device)
def __init__(self, monitor, parent=None):
"""
Observe the given ``monitor`` (a :class:`~pyudev.Monitor`):
``parent`` is the parent :class:`~PyQt4.QtCore.QObject` of this
object. It is passed unchanged to the inherited constructor of
:class:`~PyQt4.QtCore.QObject`.
"""
QObject.__init__(self, parent)
self._setup_notifier(monitor, QSocketNotifier)
<｜fim▁end｜> | """
Observe the given ``monitor`` (a :class:`~pyudev.Monitor`):
``parent`` is the parent :class:`~PyQt4.QtCore.QObject` of this
object. It is passed unchanged to the inherited constructor of
:class:`~PyQt4.QtCore.QObject`.
"""
QObject.__init__(self, parent)
self._setup_notifier(monitor, QSocketNotifier) |
<|file_name|>pyqt4.py<|end_file_name|><｜fim▁begin｜># -*- coding: utf-8 -*-
# Copyright (C) 2010, 2011, 2012, 2013 Sebastian Wiesner <[email protected]>
# This library is free software; you can redistribute it and/or modify it
# under the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation; either version 2.1 of the License, or (at your
# option) any later version.
# This library is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
# for more details.
# You should have received a copy of the GNU Lesser General Public License
# along with this library; if not, write to the Free Software Foundation,
# Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
# pylint: disable=anomalous-backslash-in-string
"""
pyudev.pyqt4
============
PyQt4 integration.
:class:`MonitorObserver` integrates device monitoring into the PyQt4\_
mainloop by turning device events into Qt signals.
:mod:`PyQt4.QtCore` from PyQt4\_ must be available when importing this
module.
.. _PyQt4: http://riverbankcomputing.co.uk/software/pyqt/intro
.. moduleauthor:: Sebastian Wiesner <[email protected]>
"""
from __future__ import (print_function, division, unicode_literals,
absolute_import)
from PyQt4.QtCore import QSocketNotifier, QObject, pyqtSignal
from pyudev._util import text_type
from pyudev.core import Device
from pyudev._qt_base import QUDevMonitorObserverMixin, MonitorObserverMixin
class MonitorObserver(QObject, MonitorObserverMixin):
"""An observer for device events integrating into the :mod:`PyQt4` mainloop.
This class inherits :class:`~PyQt4.QtCore.QObject` to turn device events
into Qt signals:
>>> from pyudev import Context, Monitor
>>> from pyudev.pyqt4 import MonitorObserver
>>> context = Context()
>>> monitor = Monitor.from_netlink(context)
>>> monitor.filter_by(subsystem='input')
>>> observer = MonitorObserver(monitor)
>>> def device_event(device):
... print('event {0} on device {1}'.format(device.action, device))
>>> observer.deviceEvent.connect(device_event)
>>> monitor.start()
This class is a child of :class:`~PyQt4.QtCore.QObject`.
"""
#: emitted upon arbitrary device events
deviceEvent = pyqtSignal(Device)
def __init__(self, monitor, parent=None):
"""
Observe the given ``monitor`` (a :class:`~pyudev.Monitor`):
``parent`` is the parent :class:`~PyQt4.QtCore.QObject` of this
object. It is passed unchanged to the inherited constructor of
:class:`~PyQt4.QtCore.QObject`.
"""
QObject.__init__(self, parent)
self._setup_notifier(monitor, QSocketNotifier)
class QUDevMonitorObserver(QObject, QUDevMonitorObserverMixin):
<|fim_middle|>
<｜fim▁end｜> | """An observer for device events integrating into the :mod:`PyQt4` mainloop.
.. deprecated:: 0.17
Will be removed in 1.0. Use :class:`MonitorObserver` instead.
"""
#: emitted upon arbitrary device events
deviceEvent = pyqtSignal(text_type, Device)
#: emitted, if a device was added
deviceAdded = pyqtSignal(Device)
#: emitted, if a device was removed
deviceRemoved = pyqtSignal(Device)
#: emitted, if a device was changed
deviceChanged = pyqtSignal(Device)
#: emitted, if a device was moved
deviceMoved = pyqtSignal(Device)
def __init__(self, monitor, parent=None):
"""
Observe the given ``monitor`` (a :class:`~pyudev.Monitor`):
``parent`` is the parent :class:`~PyQt4.QtCore.QObject` of this
object. It is passed unchanged to the inherited constructor of
:class:`~PyQt4.QtCore.QObject`.
"""
QObject.__init__(self, parent)
self._setup_notifier(monitor, QSocketNotifier) |
<|file_name|>pyqt4.py<|end_file_name|><｜fim▁begin｜># -*- coding: utf-8 -*-
# Copyright (C) 2010, 2011, 2012, 2013 Sebastian Wiesner <[email protected]>
# This library is free software; you can redistribute it and/or modify it
# under the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation; either version 2.1 of the License, or (at your
# option) any later version.
# This library is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
# for more details.
# You should have received a copy of the GNU Lesser General Public License
# along with this library; if not, write to the Free Software Foundation,
# Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
# pylint: disable=anomalous-backslash-in-string
"""
pyudev.pyqt4
============
PyQt4 integration.
:class:`MonitorObserver` integrates device monitoring into the PyQt4\_
mainloop by turning device events into Qt signals.
:mod:`PyQt4.QtCore` from PyQt4\_ must be available when importing this
module.
.. _PyQt4: http://riverbankcomputing.co.uk/software/pyqt/intro
.. moduleauthor:: Sebastian Wiesner <[email protected]>
"""
from __future__ import (print_function, division, unicode_literals,
absolute_import)
from PyQt4.QtCore import QSocketNotifier, QObject, pyqtSignal
from pyudev._util import text_type
from pyudev.core import Device
from pyudev._qt_base import QUDevMonitorObserverMixin, MonitorObserverMixin
class MonitorObserver(QObject, MonitorObserverMixin):
"""An observer for device events integrating into the :mod:`PyQt4` mainloop.
This class inherits :class:`~PyQt4.QtCore.QObject` to turn device events
into Qt signals:
>>> from pyudev import Context, Monitor
>>> from pyudev.pyqt4 import MonitorObserver
>>> context = Context()
>>> monitor = Monitor.from_netlink(context)
>>> monitor.filter_by(subsystem='input')
>>> observer = MonitorObserver(monitor)
>>> def device_event(device):
... print('event {0} on device {1}'.format(device.action, device))
>>> observer.deviceEvent.connect(device_event)
>>> monitor.start()
This class is a child of :class:`~PyQt4.QtCore.QObject`.
"""
#: emitted upon arbitrary device events
deviceEvent = pyqtSignal(Device)
def __init__(self, monitor, parent=None):
"""
Observe the given ``monitor`` (a :class:`~pyudev.Monitor`):
``parent`` is the parent :class:`~PyQt4.QtCore.QObject` of this
object. It is passed unchanged to the inherited constructor of
:class:`~PyQt4.QtCore.QObject`.
"""
QObject.__init__(self, parent)
self._setup_notifier(monitor, QSocketNotifier)
class QUDevMonitorObserver(QObject, QUDevMonitorObserverMixin):
"""An observer for device events integrating into the :mod:`PyQt4` mainloop.
.. deprecated:: 0.17
Will be removed in 1.0. Use :class:`MonitorObserver` instead.
"""
#: emitted upon arbitrary device events
deviceEvent = pyqtSignal(text_type, Device)
#: emitted, if a device was added
deviceAdded = pyqtSignal(Device)
#: emitted, if a device was removed
deviceRemoved = pyqtSignal(Device)
#: emitted, if a device was changed
deviceChanged = pyqtSignal(Device)
#: emitted, if a device was moved
deviceMoved = pyqtSignal(Device)
def __init__(self, monitor, parent=None):
<|fim_middle|>
<｜fim▁end｜> | """
Observe the given ``monitor`` (a :class:`~pyudev.Monitor`):
``parent`` is the parent :class:`~PyQt4.QtCore.QObject` of this
object. It is passed unchanged to the inherited constructor of
:class:`~PyQt4.QtCore.QObject`.
"""
QObject.__init__(self, parent)
self._setup_notifier(monitor, QSocketNotifier) |
<|file_name|>pyqt4.py<|end_file_name|><｜fim▁begin｜># -*- coding: utf-8 -*-
# Copyright (C) 2010, 2011, 2012, 2013 Sebastian Wiesner <[email protected]>
# This library is free software; you can redistribute it and/or modify it
# under the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation; either version 2.1 of the License, or (at your
# option) any later version.
# This library is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
# for more details.
# You should have received a copy of the GNU Lesser General Public License
# along with this library; if not, write to the Free Software Foundation,
# Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
# pylint: disable=anomalous-backslash-in-string
"""
pyudev.pyqt4
============
PyQt4 integration.
:class:`MonitorObserver` integrates device monitoring into the PyQt4\_
mainloop by turning device events into Qt signals.
:mod:`PyQt4.QtCore` from PyQt4\_ must be available when importing this
module.
.. _PyQt4: http://riverbankcomputing.co.uk/software/pyqt/intro
.. moduleauthor:: Sebastian Wiesner <[email protected]>
"""
from __future__ import (print_function, division, unicode_literals,
absolute_import)
from PyQt4.QtCore import QSocketNotifier, QObject, pyqtSignal
from pyudev._util import text_type
from pyudev.core import Device
from pyudev._qt_base import QUDevMonitorObserverMixin, MonitorObserverMixin
class MonitorObserver(QObject, MonitorObserverMixin):
"""An observer for device events integrating into the :mod:`PyQt4` mainloop.
This class inherits :class:`~PyQt4.QtCore.QObject` to turn device events
into Qt signals:
>>> from pyudev import Context, Monitor
>>> from pyudev.pyqt4 import MonitorObserver
>>> context = Context()
>>> monitor = Monitor.from_netlink(context)
>>> monitor.filter_by(subsystem='input')
>>> observer = MonitorObserver(monitor)
>>> def device_event(device):
... print('event {0} on device {1}'.format(device.action, device))
>>> observer.deviceEvent.connect(device_event)
>>> monitor.start()
This class is a child of :class:`~PyQt4.QtCore.QObject`.
"""
#: emitted upon arbitrary device events
deviceEvent = pyqtSignal(Device)
def <|fim_middle|>(self, monitor, parent=None):
"""
Observe the given ``monitor`` (a :class:`~pyudev.Monitor`):
``parent`` is the parent :class:`~PyQt4.QtCore.QObject` of this
object. It is passed unchanged to the inherited constructor of
:class:`~PyQt4.QtCore.QObject`.
"""
QObject.__init__(self, parent)
self._setup_notifier(monitor, QSocketNotifier)
class QUDevMonitorObserver(QObject, QUDevMonitorObserverMixin):
"""An observer for device events integrating into the :mod:`PyQt4` mainloop.
.. deprecated:: 0.17
Will be removed in 1.0. Use :class:`MonitorObserver` instead.
"""
#: emitted upon arbitrary device events
deviceEvent = pyqtSignal(text_type, Device)
#: emitted, if a device was added
deviceAdded = pyqtSignal(Device)
#: emitted, if a device was removed
deviceRemoved = pyqtSignal(Device)
#: emitted, if a device was changed
deviceChanged = pyqtSignal(Device)
#: emitted, if a device was moved
deviceMoved = pyqtSignal(Device)
def __init__(self, monitor, parent=None):
"""
Observe the given ``monitor`` (a :class:`~pyudev.Monitor`):
``parent`` is the parent :class:`~PyQt4.QtCore.QObject` of this
object. It is passed unchanged to the inherited constructor of
:class:`~PyQt4.QtCore.QObject`.
"""
QObject.__init__(self, parent)
self._setup_notifier(monitor, QSocketNotifier)
<｜fim▁end｜> | __init__ |
<|file_name|>pyqt4.py<|end_file_name|><｜fim▁begin｜># -*- coding: utf-8 -*-
# Copyright (C) 2010, 2011, 2012, 2013 Sebastian Wiesner <[email protected]>
# This library is free software; you can redistribute it and/or modify it
# under the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation; either version 2.1 of the License, or (at your
# option) any later version.
# This library is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
# for more details.
# You should have received a copy of the GNU Lesser General Public License
# along with this library; if not, write to the Free Software Foundation,
# Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
# pylint: disable=anomalous-backslash-in-string
"""
pyudev.pyqt4
============
PyQt4 integration.
:class:`MonitorObserver` integrates device monitoring into the PyQt4\_
mainloop by turning device events into Qt signals.
:mod:`PyQt4.QtCore` from PyQt4\_ must be available when importing this
module.
.. _PyQt4: http://riverbankcomputing.co.uk/software/pyqt/intro
.. moduleauthor:: Sebastian Wiesner <[email protected]>
"""
from __future__ import (print_function, division, unicode_literals,
absolute_import)
from PyQt4.QtCore import QSocketNotifier, QObject, pyqtSignal
from pyudev._util import text_type
from pyudev.core import Device
from pyudev._qt_base import QUDevMonitorObserverMixin, MonitorObserverMixin
class MonitorObserver(QObject, MonitorObserverMixin):
"""An observer for device events integrating into the :mod:`PyQt4` mainloop.
This class inherits :class:`~PyQt4.QtCore.QObject` to turn device events
into Qt signals:
>>> from pyudev import Context, Monitor
>>> from pyudev.pyqt4 import MonitorObserver
>>> context = Context()
>>> monitor = Monitor.from_netlink(context)
>>> monitor.filter_by(subsystem='input')
>>> observer = MonitorObserver(monitor)
>>> def device_event(device):
... print('event {0} on device {1}'.format(device.action, device))
>>> observer.deviceEvent.connect(device_event)
>>> monitor.start()
This class is a child of :class:`~PyQt4.QtCore.QObject`.
"""
#: emitted upon arbitrary device events
deviceEvent = pyqtSignal(Device)
def __init__(self, monitor, parent=None):
"""
Observe the given ``monitor`` (a :class:`~pyudev.Monitor`):
``parent`` is the parent :class:`~PyQt4.QtCore.QObject` of this
object. It is passed unchanged to the inherited constructor of
:class:`~PyQt4.QtCore.QObject`.
"""
QObject.__init__(self, parent)
self._setup_notifier(monitor, QSocketNotifier)
class QUDevMonitorObserver(QObject, QUDevMonitorObserverMixin):
"""An observer for device events integrating into the :mod:`PyQt4` mainloop.
.. deprecated:: 0.17
Will be removed in 1.0. Use :class:`MonitorObserver` instead.
"""
#: emitted upon arbitrary device events
deviceEvent = pyqtSignal(text_type, Device)
#: emitted, if a device was added
deviceAdded = pyqtSignal(Device)
#: emitted, if a device was removed
deviceRemoved = pyqtSignal(Device)
#: emitted, if a device was changed
deviceChanged = pyqtSignal(Device)
#: emitted, if a device was moved
deviceMoved = pyqtSignal(Device)
def <|fim_middle|>(self, monitor, parent=None):
"""
Observe the given ``monitor`` (a :class:`~pyudev.Monitor`):
``parent`` is the parent :class:`~PyQt4.QtCore.QObject` of this
object. It is passed unchanged to the inherited constructor of
:class:`~PyQt4.QtCore.QObject`.
"""
QObject.__init__(self, parent)
self._setup_notifier(monitor, QSocketNotifier)
<｜fim▁end｜> | __init__ |
<|file_name|>test_task_manager.py<|end_file_name|><｜fim▁begin｜># This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
from unittest import mock
from configman.dotdict import DotDict
from socorro.lib.task_manager import TaskManager, default_task_func
class TestTaskManager:
def test_constuctor1(self):
config = DotDict()
config.quit_on_empty_queue = False
tm = TaskManager(config)
assert tm.config == config
assert tm.task_func == default_task_func
assert tm.quit is False
def test_get_iterator(self):
config = DotDict()
config.quit_on_empty_queue = False
tm = TaskManager(config, job_source_iterator=range(1))
assert list(tm._get_iterator()) == [0]
def an_iter(self):
yield from range(5)
tm = TaskManager(config, job_source_iterator=an_iter)
assert list(tm._get_iterator()) == [0, 1, 2, 3, 4]
class X:
def __init__(self, config):
self.config = config
def __iter__(self):
yield from self.config
tm = TaskManager(config, job_source_iterator=X(config))
assert list(tm._get_iterator()) == list(config.keys())
def test_blocking_start(self):
config = DotDict()
config.idle_delay = 1
config.quit_on_empty_queue = False
class MyTaskManager(TaskManager):
def _responsive_sleep(self, seconds, wait_log_interval=0, wait_reason=""):
try:
if self.count >= 2:
raise KeyboardInterrupt
self.count += 1
except AttributeError:<｜fim▁hole｜>
waiting_func = mock.Mock()
tm.blocking_start(waiting_func=waiting_func)
assert tm.task_func.call_count == 10
assert waiting_func.call_count == 0
def test_blocking_start_with_quit_on_empty(self):
config = DotDict()
config.idle_delay = 1
config.quit_on_empty_queue = True
tm = TaskManager(config, task_func=mock.Mock())
waiting_func = mock.Mock()
tm.blocking_start(waiting_func=waiting_func)
assert tm.task_func.call_count == 10
assert waiting_func.call_count == 0<｜fim▁end｜> | self.count = 0
tm = MyTaskManager(config, task_func=mock.Mock()) |
<|file_name|>test_task_manager.py<|end_file_name|><｜fim▁begin｜># This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
from unittest import mock
from configman.dotdict import DotDict
from socorro.lib.task_manager import TaskManager, default_task_func
class TestTaskManager:
<|fim_middle|>
<｜fim▁end｜> | def test_constuctor1(self):
config = DotDict()
config.quit_on_empty_queue = False
tm = TaskManager(config)
assert tm.config == config
assert tm.task_func == default_task_func
assert tm.quit is False
def test_get_iterator(self):
config = DotDict()
config.quit_on_empty_queue = False
tm = TaskManager(config, job_source_iterator=range(1))
assert list(tm._get_iterator()) == [0]
def an_iter(self):
yield from range(5)
tm = TaskManager(config, job_source_iterator=an_iter)
assert list(tm._get_iterator()) == [0, 1, 2, 3, 4]
class X:
def __init__(self, config):
self.config = config
def __iter__(self):
yield from self.config
tm = TaskManager(config, job_source_iterator=X(config))
assert list(tm._get_iterator()) == list(config.keys())
def test_blocking_start(self):
config = DotDict()
config.idle_delay = 1
config.quit_on_empty_queue = False
class MyTaskManager(TaskManager):
def _responsive_sleep(self, seconds, wait_log_interval=0, wait_reason=""):
try:
if self.count >= 2:
raise KeyboardInterrupt
self.count += 1
except AttributeError:
self.count = 0
tm = MyTaskManager(config, task_func=mock.Mock())
waiting_func = mock.Mock()
tm.blocking_start(waiting_func=waiting_func)
assert tm.task_func.call_count == 10
assert waiting_func.call_count == 0
def test_blocking_start_with_quit_on_empty(self):
config = DotDict()
config.idle_delay = 1
config.quit_on_empty_queue = True
tm = TaskManager(config, task_func=mock.Mock())
waiting_func = mock.Mock()
tm.blocking_start(waiting_func=waiting_func)
assert tm.task_func.call_count == 10
assert waiting_func.call_count == 0 |
<|file_name|>test_task_manager.py<|end_file_name|><｜fim▁begin｜># This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
from unittest import mock
from configman.dotdict import DotDict
from socorro.lib.task_manager import TaskManager, default_task_func
class TestTaskManager:
def test_constuctor1(self):
<|fim_middle|>
def test_get_iterator(self):
config = DotDict()
config.quit_on_empty_queue = False
tm = TaskManager(config, job_source_iterator=range(1))
assert list(tm._get_iterator()) == [0]
def an_iter(self):
yield from range(5)
tm = TaskManager(config, job_source_iterator=an_iter)
assert list(tm._get_iterator()) == [0, 1, 2, 3, 4]
class X:
def __init__(self, config):
self.config = config
def __iter__(self):
yield from self.config
tm = TaskManager(config, job_source_iterator=X(config))
assert list(tm._get_iterator()) == list(config.keys())
def test_blocking_start(self):
config = DotDict()
config.idle_delay = 1
config.quit_on_empty_queue = False
class MyTaskManager(TaskManager):
def _responsive_sleep(self, seconds, wait_log_interval=0, wait_reason=""):
try:
if self.count >= 2:
raise KeyboardInterrupt
self.count += 1
except AttributeError:
self.count = 0
tm = MyTaskManager(config, task_func=mock.Mock())
waiting_func = mock.Mock()
tm.blocking_start(waiting_func=waiting_func)
assert tm.task_func.call_count == 10
assert waiting_func.call_count == 0
def test_blocking_start_with_quit_on_empty(self):
config = DotDict()
config.idle_delay = 1
config.quit_on_empty_queue = True
tm = TaskManager(config, task_func=mock.Mock())
waiting_func = mock.Mock()
tm.blocking_start(waiting_func=waiting_func)
assert tm.task_func.call_count == 10
assert waiting_func.call_count == 0
<｜fim▁end｜> | config = DotDict()
config.quit_on_empty_queue = False
tm = TaskManager(config)
assert tm.config == config
assert tm.task_func == default_task_func
assert tm.quit is False |
<|file_name|>test_task_manager.py<|end_file_name|><｜fim▁begin｜># This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
from unittest import mock
from configman.dotdict import DotDict
from socorro.lib.task_manager import TaskManager, default_task_func
class TestTaskManager:
def test_constuctor1(self):
config = DotDict()
config.quit_on_empty_queue = False
tm = TaskManager(config)
assert tm.config == config
assert tm.task_func == default_task_func
assert tm.quit is False
def test_get_iterator(self):
<|fim_middle|>
def test_blocking_start(self):
config = DotDict()
config.idle_delay = 1
config.quit_on_empty_queue = False
class MyTaskManager(TaskManager):
def _responsive_sleep(self, seconds, wait_log_interval=0, wait_reason=""):
try:
if self.count >= 2:
raise KeyboardInterrupt
self.count += 1
except AttributeError:
self.count = 0
tm = MyTaskManager(config, task_func=mock.Mock())
waiting_func = mock.Mock()
tm.blocking_start(waiting_func=waiting_func)
assert tm.task_func.call_count == 10
assert waiting_func.call_count == 0
def test_blocking_start_with_quit_on_empty(self):
config = DotDict()
config.idle_delay = 1
config.quit_on_empty_queue = True
tm = TaskManager(config, task_func=mock.Mock())
waiting_func = mock.Mock()
tm.blocking_start(waiting_func=waiting_func)
assert tm.task_func.call_count == 10
assert waiting_func.call_count == 0
<｜fim▁end｜> | config = DotDict()
config.quit_on_empty_queue = False
tm = TaskManager(config, job_source_iterator=range(1))
assert list(tm._get_iterator()) == [0]
def an_iter(self):
yield from range(5)
tm = TaskManager(config, job_source_iterator=an_iter)
assert list(tm._get_iterator()) == [0, 1, 2, 3, 4]
class X:
def __init__(self, config):
self.config = config
def __iter__(self):
yield from self.config
tm = TaskManager(config, job_source_iterator=X(config))
assert list(tm._get_iterator()) == list(config.keys()) |
<|file_name|>test_task_manager.py<|end_file_name|><｜fim▁begin｜># This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
from unittest import mock
from configman.dotdict import DotDict
from socorro.lib.task_manager import TaskManager, default_task_func
class TestTaskManager:
def test_constuctor1(self):
config = DotDict()
config.quit_on_empty_queue = False
tm = TaskManager(config)
assert tm.config == config
assert tm.task_func == default_task_func
assert tm.quit is False
def test_get_iterator(self):
config = DotDict()
config.quit_on_empty_queue = False
tm = TaskManager(config, job_source_iterator=range(1))
assert list(tm._get_iterator()) == [0]
def an_iter(self):
<|fim_middle|>
tm = TaskManager(config, job_source_iterator=an_iter)
assert list(tm._get_iterator()) == [0, 1, 2, 3, 4]
class X:
def __init__(self, config):
self.config = config
def __iter__(self):
yield from self.config
tm = TaskManager(config, job_source_iterator=X(config))
assert list(tm._get_iterator()) == list(config.keys())
def test_blocking_start(self):
config = DotDict()
config.idle_delay = 1
config.quit_on_empty_queue = False
class MyTaskManager(TaskManager):
def _responsive_sleep(self, seconds, wait_log_interval=0, wait_reason=""):
try:
if self.count >= 2:
raise KeyboardInterrupt
self.count += 1
except AttributeError:
self.count = 0
tm = MyTaskManager(config, task_func=mock.Mock())
waiting_func = mock.Mock()
tm.blocking_start(waiting_func=waiting_func)
assert tm.task_func.call_count == 10
assert waiting_func.call_count == 0
def test_blocking_start_with_quit_on_empty(self):
config = DotDict()
config.idle_delay = 1
config.quit_on_empty_queue = True
tm = TaskManager(config, task_func=mock.Mock())
waiting_func = mock.Mock()
tm.blocking_start(waiting_func=waiting_func)
assert tm.task_func.call_count == 10
assert waiting_func.call_count == 0
<｜fim▁end｜> | yield from range(5) |
<|file_name|>test_task_manager.py<|end_file_name|><｜fim▁begin｜># This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
from unittest import mock
from configman.dotdict import DotDict
from socorro.lib.task_manager import TaskManager, default_task_func
class TestTaskManager:
def test_constuctor1(self):
config = DotDict()
config.quit_on_empty_queue = False
tm = TaskManager(config)
assert tm.config == config
assert tm.task_func == default_task_func
assert tm.quit is False
def test_get_iterator(self):
config = DotDict()
config.quit_on_empty_queue = False
tm = TaskManager(config, job_source_iterator=range(1))
assert list(tm._get_iterator()) == [0]
def an_iter(self):
yield from range(5)
tm = TaskManager(config, job_source_iterator=an_iter)
assert list(tm._get_iterator()) == [0, 1, 2, 3, 4]
class X:
<|fim_middle|>
tm = TaskManager(config, job_source_iterator=X(config))
assert list(tm._get_iterator()) == list(config.keys())
def test_blocking_start(self):
config = DotDict()
config.idle_delay = 1
config.quit_on_empty_queue = False
class MyTaskManager(TaskManager):
def _responsive_sleep(self, seconds, wait_log_interval=0, wait_reason=""):
try:
if self.count >= 2:
raise KeyboardInterrupt
self.count += 1
except AttributeError:
self.count = 0
tm = MyTaskManager(config, task_func=mock.Mock())
waiting_func = mock.Mock()
tm.blocking_start(waiting_func=waiting_func)
assert tm.task_func.call_count == 10
assert waiting_func.call_count == 0
def test_blocking_start_with_quit_on_empty(self):
config = DotDict()
config.idle_delay = 1
config.quit_on_empty_queue = True
tm = TaskManager(config, task_func=mock.Mock())
waiting_func = mock.Mock()
tm.blocking_start(waiting_func=waiting_func)
assert tm.task_func.call_count == 10
assert waiting_func.call_count == 0
<｜fim▁end｜> | def __init__(self, config):
self.config = config
def __iter__(self):
yield from self.config |
<|file_name|>test_task_manager.py<|end_file_name|><｜fim▁begin｜># This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
from unittest import mock
from configman.dotdict import DotDict
from socorro.lib.task_manager import TaskManager, default_task_func
class TestTaskManager:
def test_constuctor1(self):
config = DotDict()
config.quit_on_empty_queue = False
tm = TaskManager(config)
assert tm.config == config
assert tm.task_func == default_task_func
assert tm.quit is False
def test_get_iterator(self):
config = DotDict()
config.quit_on_empty_queue = False
tm = TaskManager(config, job_source_iterator=range(1))
assert list(tm._get_iterator()) == [0]
def an_iter(self):
yield from range(5)
tm = TaskManager(config, job_source_iterator=an_iter)
assert list(tm._get_iterator()) == [0, 1, 2, 3, 4]
class X:
def __init__(self, config):
<|fim_middle|>
def __iter__(self):
yield from self.config
tm = TaskManager(config, job_source_iterator=X(config))
assert list(tm._get_iterator()) == list(config.keys())
def test_blocking_start(self):
config = DotDict()
config.idle_delay = 1
config.quit_on_empty_queue = False
class MyTaskManager(TaskManager):
def _responsive_sleep(self, seconds, wait_log_interval=0, wait_reason=""):
try:
if self.count >= 2:
raise KeyboardInterrupt
self.count += 1
except AttributeError:
self.count = 0
tm = MyTaskManager(config, task_func=mock.Mock())
waiting_func = mock.Mock()
tm.blocking_start(waiting_func=waiting_func)
assert tm.task_func.call_count == 10
assert waiting_func.call_count == 0
def test_blocking_start_with_quit_on_empty(self):
config = DotDict()
config.idle_delay = 1
config.quit_on_empty_queue = True
tm = TaskManager(config, task_func=mock.Mock())
waiting_func = mock.Mock()
tm.blocking_start(waiting_func=waiting_func)
assert tm.task_func.call_count == 10
assert waiting_func.call_count == 0
<｜fim▁end｜> | self.config = config |
<|file_name|>test_task_manager.py<|end_file_name|><｜fim▁begin｜># This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
from unittest import mock
from configman.dotdict import DotDict
from socorro.lib.task_manager import TaskManager, default_task_func
class TestTaskManager:
def test_constuctor1(self):
config = DotDict()
config.quit_on_empty_queue = False
tm = TaskManager(config)
assert tm.config == config
assert tm.task_func == default_task_func
assert tm.quit is False
def test_get_iterator(self):
config = DotDict()
config.quit_on_empty_queue = False
tm = TaskManager(config, job_source_iterator=range(1))
assert list(tm._get_iterator()) == [0]
def an_iter(self):
yield from range(5)
tm = TaskManager(config, job_source_iterator=an_iter)
assert list(tm._get_iterator()) == [0, 1, 2, 3, 4]
class X:
def __init__(self, config):
self.config = config
def __iter__(self):
<|fim_middle|>
tm = TaskManager(config, job_source_iterator=X(config))
assert list(tm._get_iterator()) == list(config.keys())
def test_blocking_start(self):
config = DotDict()
config.idle_delay = 1
config.quit_on_empty_queue = False
class MyTaskManager(TaskManager):
def _responsive_sleep(self, seconds, wait_log_interval=0, wait_reason=""):
try:
if self.count >= 2:
raise KeyboardInterrupt
self.count += 1
except AttributeError:
self.count = 0
tm = MyTaskManager(config, task_func=mock.Mock())
waiting_func = mock.Mock()
tm.blocking_start(waiting_func=waiting_func)
assert tm.task_func.call_count == 10
assert waiting_func.call_count == 0
def test_blocking_start_with_quit_on_empty(self):
config = DotDict()
config.idle_delay = 1
config.quit_on_empty_queue = True
tm = TaskManager(config, task_func=mock.Mock())
waiting_func = mock.Mock()
tm.blocking_start(waiting_func=waiting_func)
assert tm.task_func.call_count == 10
assert waiting_func.call_count == 0
<｜fim▁end｜> | yield from self.config |
<|file_name|>test_task_manager.py<|end_file_name|><｜fim▁begin｜># This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
from unittest import mock
from configman.dotdict import DotDict
from socorro.lib.task_manager import TaskManager, default_task_func
class TestTaskManager:
def test_constuctor1(self):
config = DotDict()
config.quit_on_empty_queue = False
tm = TaskManager(config)
assert tm.config == config
assert tm.task_func == default_task_func
assert tm.quit is False
def test_get_iterator(self):
config = DotDict()
config.quit_on_empty_queue = False
tm = TaskManager(config, job_source_iterator=range(1))
assert list(tm._get_iterator()) == [0]
def an_iter(self):
yield from range(5)
tm = TaskManager(config, job_source_iterator=an_iter)
assert list(tm._get_iterator()) == [0, 1, 2, 3, 4]
class X:
def __init__(self, config):
self.config = config
def __iter__(self):
yield from self.config
tm = TaskManager(config, job_source_iterator=X(config))
assert list(tm._get_iterator()) == list(config.keys())
def test_blocking_start(self):
<|fim_middle|>
def test_blocking_start_with_quit_on_empty(self):
config = DotDict()
config.idle_delay = 1
config.quit_on_empty_queue = True
tm = TaskManager(config, task_func=mock.Mock())
waiting_func = mock.Mock()
tm.blocking_start(waiting_func=waiting_func)
assert tm.task_func.call_count == 10
assert waiting_func.call_count == 0
<｜fim▁end｜> | config = DotDict()
config.idle_delay = 1
config.quit_on_empty_queue = False
class MyTaskManager(TaskManager):
def _responsive_sleep(self, seconds, wait_log_interval=0, wait_reason=""):
try:
if self.count >= 2:
raise KeyboardInterrupt
self.count += 1
except AttributeError:
self.count = 0
tm = MyTaskManager(config, task_func=mock.Mock())
waiting_func = mock.Mock()
tm.blocking_start(waiting_func=waiting_func)
assert tm.task_func.call_count == 10
assert waiting_func.call_count == 0 |
<|file_name|>test_task_manager.py<|end_file_name|><｜fim▁begin｜># This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
from unittest import mock
from configman.dotdict import DotDict
from socorro.lib.task_manager import TaskManager, default_task_func
class TestTaskManager:
def test_constuctor1(self):
config = DotDict()
config.quit_on_empty_queue = False
tm = TaskManager(config)
assert tm.config == config
assert tm.task_func == default_task_func
assert tm.quit is False
def test_get_iterator(self):
config = DotDict()
config.quit_on_empty_queue = False
tm = TaskManager(config, job_source_iterator=range(1))
assert list(tm._get_iterator()) == [0]
def an_iter(self):
yield from range(5)
tm = TaskManager(config, job_source_iterator=an_iter)
assert list(tm._get_iterator()) == [0, 1, 2, 3, 4]
class X:
def __init__(self, config):
self.config = config
def __iter__(self):
yield from self.config
tm = TaskManager(config, job_source_iterator=X(config))
assert list(tm._get_iterator()) == list(config.keys())
def test_blocking_start(self):
config = DotDict()
config.idle_delay = 1
config.quit_on_empty_queue = False
class MyTaskManager(TaskManager):
<|fim_middle|>
tm = MyTaskManager(config, task_func=mock.Mock())
waiting_func = mock.Mock()
tm.blocking_start(waiting_func=waiting_func)
assert tm.task_func.call_count == 10
assert waiting_func.call_count == 0
def test_blocking_start_with_quit_on_empty(self):
config = DotDict()
config.idle_delay = 1
config.quit_on_empty_queue = True
tm = TaskManager(config, task_func=mock.Mock())
waiting_func = mock.Mock()
tm.blocking_start(waiting_func=waiting_func)
assert tm.task_func.call_count == 10
assert waiting_func.call_count == 0
<｜fim▁end｜> | def _responsive_sleep(self, seconds, wait_log_interval=0, wait_reason=""):
try:
if self.count >= 2:
raise KeyboardInterrupt
self.count += 1
except AttributeError:
self.count = 0 |
<|file_name|>test_task_manager.py<|end_file_name|><｜fim▁begin｜># This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
from unittest import mock
from configman.dotdict import DotDict
from socorro.lib.task_manager import TaskManager, default_task_func
class TestTaskManager:
def test_constuctor1(self):
config = DotDict()
config.quit_on_empty_queue = False
tm = TaskManager(config)
assert tm.config == config
assert tm.task_func == default_task_func
assert tm.quit is False
def test_get_iterator(self):
config = DotDict()
config.quit_on_empty_queue = False
tm = TaskManager(config, job_source_iterator=range(1))
assert list(tm._get_iterator()) == [0]
def an_iter(self):
yield from range(5)
tm = TaskManager(config, job_source_iterator=an_iter)
assert list(tm._get_iterator()) == [0, 1, 2, 3, 4]
class X:
def __init__(self, config):
self.config = config
def __iter__(self):
yield from self.config
tm = TaskManager(config, job_source_iterator=X(config))
assert list(tm._get_iterator()) == list(config.keys())
def test_blocking_start(self):
config = DotDict()
config.idle_delay = 1
config.quit_on_empty_queue = False
class MyTaskManager(TaskManager):
def _responsive_sleep(self, seconds, wait_log_interval=0, wait_reason=""):
<|fim_middle|>
tm = MyTaskManager(config, task_func=mock.Mock())
waiting_func = mock.Mock()
tm.blocking_start(waiting_func=waiting_func)
assert tm.task_func.call_count == 10
assert waiting_func.call_count == 0
def test_blocking_start_with_quit_on_empty(self):
config = DotDict()
config.idle_delay = 1
config.quit_on_empty_queue = True
tm = TaskManager(config, task_func=mock.Mock())
waiting_func = mock.Mock()
tm.blocking_start(waiting_func=waiting_func)
assert tm.task_func.call_count == 10
assert waiting_func.call_count == 0
<｜fim▁end｜> | try:
if self.count >= 2:
raise KeyboardInterrupt
self.count += 1
except AttributeError:
self.count = 0 |
<|file_name|>test_task_manager.py<|end_file_name|><｜fim▁begin｜># This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
from unittest import mock
from configman.dotdict import DotDict
from socorro.lib.task_manager import TaskManager, default_task_func
class TestTaskManager:
def test_constuctor1(self):
config = DotDict()
config.quit_on_empty_queue = False
tm = TaskManager(config)
assert tm.config == config
assert tm.task_func == default_task_func
assert tm.quit is False
def test_get_iterator(self):
config = DotDict()
config.quit_on_empty_queue = False
tm = TaskManager(config, job_source_iterator=range(1))
assert list(tm._get_iterator()) == [0]
def an_iter(self):
yield from range(5)
tm = TaskManager(config, job_source_iterator=an_iter)
assert list(tm._get_iterator()) == [0, 1, 2, 3, 4]
class X:
def __init__(self, config):
self.config = config
def __iter__(self):
yield from self.config
tm = TaskManager(config, job_source_iterator=X(config))
assert list(tm._get_iterator()) == list(config.keys())
def test_blocking_start(self):
config = DotDict()
config.idle_delay = 1
config.quit_on_empty_queue = False
class MyTaskManager(TaskManager):
def _responsive_sleep(self, seconds, wait_log_interval=0, wait_reason=""):
try:
if self.count >= 2:
raise KeyboardInterrupt
self.count += 1
except AttributeError:
self.count = 0
tm = MyTaskManager(config, task_func=mock.Mock())
waiting_func = mock.Mock()
tm.blocking_start(waiting_func=waiting_func)
assert tm.task_func.call_count == 10
assert waiting_func.call_count == 0
def test_blocking_start_with_quit_on_empty(self):
<|fim_middle|>
<｜fim▁end｜> | config = DotDict()
config.idle_delay = 1
config.quit_on_empty_queue = True
tm = TaskManager(config, task_func=mock.Mock())
waiting_func = mock.Mock()
tm.blocking_start(waiting_func=waiting_func)
assert tm.task_func.call_count == 10
assert waiting_func.call_count == 0 |
<|file_name|>test_task_manager.py<|end_file_name|><｜fim▁begin｜># This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
from unittest import mock
from configman.dotdict import DotDict
from socorro.lib.task_manager import TaskManager, default_task_func
class TestTaskManager:
def test_constuctor1(self):
config = DotDict()
config.quit_on_empty_queue = False
tm = TaskManager(config)
assert tm.config == config
assert tm.task_func == default_task_func
assert tm.quit is False
def test_get_iterator(self):
config = DotDict()
config.quit_on_empty_queue = False
tm = TaskManager(config, job_source_iterator=range(1))
assert list(tm._get_iterator()) == [0]
def an_iter(self):
yield from range(5)
tm = TaskManager(config, job_source_iterator=an_iter)
assert list(tm._get_iterator()) == [0, 1, 2, 3, 4]
class X:
def __init__(self, config):
self.config = config
def __iter__(self):
yield from self.config
tm = TaskManager(config, job_source_iterator=X(config))
assert list(tm._get_iterator()) == list(config.keys())
def test_blocking_start(self):
config = DotDict()
config.idle_delay = 1
config.quit_on_empty_queue = False
class MyTaskManager(TaskManager):
def _responsive_sleep(self, seconds, wait_log_interval=0, wait_reason=""):
try:
if self.count >= 2:
<|fim_middle|>
self.count += 1
except AttributeError:
self.count = 0
tm = MyTaskManager(config, task_func=mock.Mock())
waiting_func = mock.Mock()
tm.blocking_start(waiting_func=waiting_func)
assert tm.task_func.call_count == 10
assert waiting_func.call_count == 0
def test_blocking_start_with_quit_on_empty(self):
config = DotDict()
config.idle_delay = 1
config.quit_on_empty_queue = True
tm = TaskManager(config, task_func=mock.Mock())
waiting_func = mock.Mock()
tm.blocking_start(waiting_func=waiting_func)
assert tm.task_func.call_count == 10
assert waiting_func.call_count == 0
<｜fim▁end｜> | raise KeyboardInterrupt |
<|file_name|>test_task_manager.py<|end_file_name|><｜fim▁begin｜># This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
from unittest import mock
from configman.dotdict import DotDict
from socorro.lib.task_manager import TaskManager, default_task_func
class TestTaskManager:
def <|fim_middle|>(self):
config = DotDict()
config.quit_on_empty_queue = False
tm = TaskManager(config)
assert tm.config == config
assert tm.task_func == default_task_func
assert tm.quit is False
def test_get_iterator(self):
config = DotDict()
config.quit_on_empty_queue = False
tm = TaskManager(config, job_source_iterator=range(1))
assert list(tm._get_iterator()) == [0]
def an_iter(self):
yield from range(5)
tm = TaskManager(config, job_source_iterator=an_iter)
assert list(tm._get_iterator()) == [0, 1, 2, 3, 4]
class X:
def __init__(self, config):
self.config = config
def __iter__(self):
yield from self.config
tm = TaskManager(config, job_source_iterator=X(config))
assert list(tm._get_iterator()) == list(config.keys())
def test_blocking_start(self):
config = DotDict()
config.idle_delay = 1
config.quit_on_empty_queue = False
class MyTaskManager(TaskManager):
def _responsive_sleep(self, seconds, wait_log_interval=0, wait_reason=""):
try:
if self.count >= 2:
raise KeyboardInterrupt
self.count += 1
except AttributeError:
self.count = 0
tm = MyTaskManager(config, task_func=mock.Mock())
waiting_func = mock.Mock()
tm.blocking_start(waiting_func=waiting_func)
assert tm.task_func.call_count == 10
assert waiting_func.call_count == 0
def test_blocking_start_with_quit_on_empty(self):
config = DotDict()
config.idle_delay = 1
config.quit_on_empty_queue = True
tm = TaskManager(config, task_func=mock.Mock())
waiting_func = mock.Mock()
tm.blocking_start(waiting_func=waiting_func)
assert tm.task_func.call_count == 10
assert waiting_func.call_count == 0
<｜fim▁end｜> | test_constuctor1 |
<|file_name|>test_task_manager.py<|end_file_name|><｜fim▁begin｜># This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
from unittest import mock
from configman.dotdict import DotDict
from socorro.lib.task_manager import TaskManager, default_task_func
class TestTaskManager:
def test_constuctor1(self):
config = DotDict()
config.quit_on_empty_queue = False
tm = TaskManager(config)
assert tm.config == config
assert tm.task_func == default_task_func
assert tm.quit is False
def <|fim_middle|>(self):
config = DotDict()
config.quit_on_empty_queue = False
tm = TaskManager(config, job_source_iterator=range(1))
assert list(tm._get_iterator()) == [0]
def an_iter(self):
yield from range(5)
tm = TaskManager(config, job_source_iterator=an_iter)
assert list(tm._get_iterator()) == [0, 1, 2, 3, 4]
class X:
def __init__(self, config):
self.config = config
def __iter__(self):
yield from self.config
tm = TaskManager(config, job_source_iterator=X(config))
assert list(tm._get_iterator()) == list(config.keys())
def test_blocking_start(self):
config = DotDict()
config.idle_delay = 1
config.quit_on_empty_queue = False
class MyTaskManager(TaskManager):
def _responsive_sleep(self, seconds, wait_log_interval=0, wait_reason=""):
try:
if self.count >= 2:
raise KeyboardInterrupt
self.count += 1
except AttributeError:
self.count = 0
tm = MyTaskManager(config, task_func=mock.Mock())
waiting_func = mock.Mock()
tm.blocking_start(waiting_func=waiting_func)
assert tm.task_func.call_count == 10
assert waiting_func.call_count == 0
def test_blocking_start_with_quit_on_empty(self):
config = DotDict()
config.idle_delay = 1
config.quit_on_empty_queue = True
tm = TaskManager(config, task_func=mock.Mock())
waiting_func = mock.Mock()
tm.blocking_start(waiting_func=waiting_func)
assert tm.task_func.call_count == 10
assert waiting_func.call_count == 0
<｜fim▁end｜> | test_get_iterator |
<|file_name|>test_task_manager.py<|end_file_name|><｜fim▁begin｜># This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
from unittest import mock
from configman.dotdict import DotDict
from socorro.lib.task_manager import TaskManager, default_task_func
class TestTaskManager:
def test_constuctor1(self):
config = DotDict()
config.quit_on_empty_queue = False
tm = TaskManager(config)
assert tm.config == config
assert tm.task_func == default_task_func
assert tm.quit is False
def test_get_iterator(self):
config = DotDict()
config.quit_on_empty_queue = False
tm = TaskManager(config, job_source_iterator=range(1))
assert list(tm._get_iterator()) == [0]
def <|fim_middle|>(self):
yield from range(5)
tm = TaskManager(config, job_source_iterator=an_iter)
assert list(tm._get_iterator()) == [0, 1, 2, 3, 4]
class X:
def __init__(self, config):
self.config = config
def __iter__(self):
yield from self.config
tm = TaskManager(config, job_source_iterator=X(config))
assert list(tm._get_iterator()) == list(config.keys())
def test_blocking_start(self):
config = DotDict()
config.idle_delay = 1
config.quit_on_empty_queue = False
class MyTaskManager(TaskManager):
def _responsive_sleep(self, seconds, wait_log_interval=0, wait_reason=""):
try:
if self.count >= 2:
raise KeyboardInterrupt
self.count += 1
except AttributeError:
self.count = 0
tm = MyTaskManager(config, task_func=mock.Mock())
waiting_func = mock.Mock()
tm.blocking_start(waiting_func=waiting_func)
assert tm.task_func.call_count == 10
assert waiting_func.call_count == 0
def test_blocking_start_with_quit_on_empty(self):
config = DotDict()
config.idle_delay = 1
config.quit_on_empty_queue = True
tm = TaskManager(config, task_func=mock.Mock())
waiting_func = mock.Mock()
tm.blocking_start(waiting_func=waiting_func)
assert tm.task_func.call_count == 10
assert waiting_func.call_count == 0
<｜fim▁end｜> | an_iter |
<|file_name|>test_task_manager.py<|end_file_name|><｜fim▁begin｜># This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
from unittest import mock
from configman.dotdict import DotDict
from socorro.lib.task_manager import TaskManager, default_task_func
class TestTaskManager:
def test_constuctor1(self):
config = DotDict()
config.quit_on_empty_queue = False
tm = TaskManager(config)
assert tm.config == config
assert tm.task_func == default_task_func
assert tm.quit is False
def test_get_iterator(self):
config = DotDict()
config.quit_on_empty_queue = False
tm = TaskManager(config, job_source_iterator=range(1))
assert list(tm._get_iterator()) == [0]
def an_iter(self):
yield from range(5)
tm = TaskManager(config, job_source_iterator=an_iter)
assert list(tm._get_iterator()) == [0, 1, 2, 3, 4]
class X:
def <|fim_middle|>(self, config):
self.config = config
def __iter__(self):
yield from self.config
tm = TaskManager(config, job_source_iterator=X(config))
assert list(tm._get_iterator()) == list(config.keys())
def test_blocking_start(self):
config = DotDict()
config.idle_delay = 1
config.quit_on_empty_queue = False
class MyTaskManager(TaskManager):
def _responsive_sleep(self, seconds, wait_log_interval=0, wait_reason=""):
try:
if self.count >= 2:
raise KeyboardInterrupt
self.count += 1
except AttributeError:
self.count = 0
tm = MyTaskManager(config, task_func=mock.Mock())
waiting_func = mock.Mock()
tm.blocking_start(waiting_func=waiting_func)
assert tm.task_func.call_count == 10
assert waiting_func.call_count == 0
def test_blocking_start_with_quit_on_empty(self):
config = DotDict()
config.idle_delay = 1
config.quit_on_empty_queue = True
tm = TaskManager(config, task_func=mock.Mock())
waiting_func = mock.Mock()
tm.blocking_start(waiting_func=waiting_func)
assert tm.task_func.call_count == 10
assert waiting_func.call_count == 0
<｜fim▁end｜> | __init__ |
<|file_name|>test_task_manager.py<|end_file_name|><｜fim▁begin｜># This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
from unittest import mock
from configman.dotdict import DotDict
from socorro.lib.task_manager import TaskManager, default_task_func
class TestTaskManager:
def test_constuctor1(self):
config = DotDict()
config.quit_on_empty_queue = False
tm = TaskManager(config)
assert tm.config == config
assert tm.task_func == default_task_func
assert tm.quit is False
def test_get_iterator(self):
config = DotDict()
config.quit_on_empty_queue = False
tm = TaskManager(config, job_source_iterator=range(1))
assert list(tm._get_iterator()) == [0]
def an_iter(self):
yield from range(5)
tm = TaskManager(config, job_source_iterator=an_iter)
assert list(tm._get_iterator()) == [0, 1, 2, 3, 4]
class X:
def __init__(self, config):
self.config = config
def <|fim_middle|>(self):
yield from self.config
tm = TaskManager(config, job_source_iterator=X(config))
assert list(tm._get_iterator()) == list(config.keys())
def test_blocking_start(self):
config = DotDict()
config.idle_delay = 1
config.quit_on_empty_queue = False
class MyTaskManager(TaskManager):
def _responsive_sleep(self, seconds, wait_log_interval=0, wait_reason=""):
try:
if self.count >= 2:
raise KeyboardInterrupt
self.count += 1
except AttributeError:
self.count = 0
tm = MyTaskManager(config, task_func=mock.Mock())
waiting_func = mock.Mock()
tm.blocking_start(waiting_func=waiting_func)
assert tm.task_func.call_count == 10
assert waiting_func.call_count == 0
def test_blocking_start_with_quit_on_empty(self):
config = DotDict()
config.idle_delay = 1
config.quit_on_empty_queue = True
tm = TaskManager(config, task_func=mock.Mock())
waiting_func = mock.Mock()
tm.blocking_start(waiting_func=waiting_func)
assert tm.task_func.call_count == 10
assert waiting_func.call_count == 0
<｜fim▁end｜> | __iter__ |
<|file_name|>test_task_manager.py<|end_file_name|><｜fim▁begin｜># This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
from unittest import mock
from configman.dotdict import DotDict
from socorro.lib.task_manager import TaskManager, default_task_func
class TestTaskManager:
def test_constuctor1(self):
config = DotDict()
config.quit_on_empty_queue = False
tm = TaskManager(config)
assert tm.config == config
assert tm.task_func == default_task_func
assert tm.quit is False
def test_get_iterator(self):
config = DotDict()
config.quit_on_empty_queue = False
tm = TaskManager(config, job_source_iterator=range(1))
assert list(tm._get_iterator()) == [0]
def an_iter(self):
yield from range(5)
tm = TaskManager(config, job_source_iterator=an_iter)
assert list(tm._get_iterator()) == [0, 1, 2, 3, 4]
class X:
def __init__(self, config):
self.config = config
def __iter__(self):
yield from self.config
tm = TaskManager(config, job_source_iterator=X(config))
assert list(tm._get_iterator()) == list(config.keys())
def <|fim_middle|>(self):
config = DotDict()
config.idle_delay = 1
config.quit_on_empty_queue = False
class MyTaskManager(TaskManager):
def _responsive_sleep(self, seconds, wait_log_interval=0, wait_reason=""):
try:
if self.count >= 2:
raise KeyboardInterrupt
self.count += 1
except AttributeError:
self.count = 0
tm = MyTaskManager(config, task_func=mock.Mock())
waiting_func = mock.Mock()
tm.blocking_start(waiting_func=waiting_func)
assert tm.task_func.call_count == 10
assert waiting_func.call_count == 0
def test_blocking_start_with_quit_on_empty(self):
config = DotDict()
config.idle_delay = 1
config.quit_on_empty_queue = True
tm = TaskManager(config, task_func=mock.Mock())
waiting_func = mock.Mock()
tm.blocking_start(waiting_func=waiting_func)
assert tm.task_func.call_count == 10
assert waiting_func.call_count == 0
<｜fim▁end｜> | test_blocking_start |
<|file_name|>test_task_manager.py<|end_file_name|><｜fim▁begin｜># This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
from unittest import mock
from configman.dotdict import DotDict
from socorro.lib.task_manager import TaskManager, default_task_func
class TestTaskManager:
def test_constuctor1(self):
config = DotDict()
config.quit_on_empty_queue = False
tm = TaskManager(config)
assert tm.config == config
assert tm.task_func == default_task_func
assert tm.quit is False
def test_get_iterator(self):
config = DotDict()
config.quit_on_empty_queue = False
tm = TaskManager(config, job_source_iterator=range(1))
assert list(tm._get_iterator()) == [0]
def an_iter(self):
yield from range(5)
tm = TaskManager(config, job_source_iterator=an_iter)
assert list(tm._get_iterator()) == [0, 1, 2, 3, 4]
class X:
def __init__(self, config):
self.config = config
def __iter__(self):
yield from self.config
tm = TaskManager(config, job_source_iterator=X(config))
assert list(tm._get_iterator()) == list(config.keys())
def test_blocking_start(self):
config = DotDict()
config.idle_delay = 1
config.quit_on_empty_queue = False
class MyTaskManager(TaskManager):
def <|fim_middle|>(self, seconds, wait_log_interval=0, wait_reason=""):
try:
if self.count >= 2:
raise KeyboardInterrupt
self.count += 1
except AttributeError:
self.count = 0
tm = MyTaskManager(config, task_func=mock.Mock())
waiting_func = mock.Mock()
tm.blocking_start(waiting_func=waiting_func)
assert tm.task_func.call_count == 10
assert waiting_func.call_count == 0
def test_blocking_start_with_quit_on_empty(self):
config = DotDict()
config.idle_delay = 1
config.quit_on_empty_queue = True
tm = TaskManager(config, task_func=mock.Mock())
waiting_func = mock.Mock()
tm.blocking_start(waiting_func=waiting_func)
assert tm.task_func.call_count == 10
assert waiting_func.call_count == 0
<｜fim▁end｜> | _responsive_sleep |
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