Update code/add_alignment.py

code/add_alignment.py

@@ -7,10 +7,9 @@ from Bio.pairwise2 import format_alignment
 
 
 def do_alignment(identifier, uniprotSequence, pdbSequence, alignment_path):
-    #print(f'Aligning Datapoint: {identifier}')
+    print(f'Aligning Datapoint: {identifier}')
     if len(pdbSequence) >= 1:
-        f = open(Path(alignment_path / f'{identifier}_alignment.txt'),
-                 "w")
+        f = open(Path(alignment_path / f'{identifier}_alignment.txt'),"w")
         aligner.mode = 'local'
         aligner.substitution_matrix = substitution_matrices.load("BLOSUM62")
         aligner.open_gap_score = -11
@@ -25,6 +24,7 @@ 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(alignment_list)
     return alignment_list
 
 
@@ -308,8 +308,11 @@ 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',i)
         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]
+        
+        print('df',df)        
         df.at[i, 'mutationPositionOnPDB'] = mutation_position_on_pdb(alignment_list, df.at[i, 'pos'])[1]
         print('df',df)
         startGap = mutation_position_on_pdb(alignment_list, df.at[i, 'pos'])[2]