Update code/add_alignment.py

code/add_alignment.py

@@ -42,10 +42,6 @@ def do_alignment(identifier, uniprotSequence, pdbSequence, alignment_path):
             alignment = (str(alignment).strip().split('\n'))
             alignment = [''.join(['.' if m == ' ' else m for m in x]) for x in alignment]
             alignment_list.append(alignment)
-    print('alignments')
-    print(alignments)
-    print('ALIGNMENT LIST')
-    print(alignment_list)
     return alignment_list
     
 
@@ -113,12 +109,6 @@ def mutation_position_on_pdb(alignment_list, pos):
         else:
             pdb_alignStatus = 'not_aligned'
             mutationPositionOnPDB = 'nan'
-    print()
-    print('-----')
-    print('ALIGNMENT STATUS')
-    print(pdb_alignStatus, mutationPositionOnPDB, startGap, alignment_list[which_alignment_to_go - 1])
-    print('-----')
-    print()
     return (pdb_alignStatus, mutationPositionOnPDB, startGap, alignment_list[which_alignment_to_go - 1])
 
 
@@ -332,9 +322,7 @@ def annotation_pos_on_pdb(annot_positions, startGap, alignment_to_use, identifie
 
 def final_stage(df, annotation_list, alignment_path):
     for i in df.index:
-        print('i',i)
         identifier = df.at[i, 'uniprotID'] + '_' + df.at[i, 'pdbID'] + '_' + df.at[i, 'chain'] + '_'
-        print('i',identifier)
         alignment_list = do_alignment(identifier, df.at[i, 'uniprotSequence'], df.at[i, 'pdbSequence'], alignment_path)
         df.at[i, 'pdb_alignStatus'] = mutation_position_on_pdb(alignment_list, df.at[i, 'pos'])[0]
         df.at[i, 'mutationPositionOnPDB'] = mutation_position_on_pdb(alignment_list, df.at[i, 'pos'])[1]
@@ -353,8 +341,6 @@ def final_stage(df, annotation_list, alignment_path):
                 str(df.at[i, 'domStart']) != '-1.0' or str(df.at[i, 'domEnd']) != '-1.0':
             df.at[i, 'domainStartonPDB'] = 'nan'
             df.at[i, 'domainEndonPDB'] = 'nan'
-    print('Final Stage')
-    print(df.to_string())
     return df
 
 def alignment(dataframe_to_align, annotation_list, alignment_path):