Update code/add_alignment.py

code/add_alignment.py

@@ -14,9 +14,13 @@ def do_alignment(identifier, uniprotSequence, pdbSequence, alignment_path):
     #if len(pdbSequence) >= 1:
     #f = open(Path(alignment_path / f'{identifier}_alignment.txt'),"w")
     aligner.mode = 'local'
+    print('1')
     aligner.substitution_matrix = substitution_matrices.load("BLOSUM62")
+    print('2')
     aligner.open_gap_score = -11
+    print('3')
     aligner.extend_gap_score = -1
+    print('4')
     alignments = aligner.align(uniprotSequence, pdbSequence)
     print('Alignments')
     print(alignments)