Update code/add_alignment.py

code/add_alignment.py

@@ -28,32 +28,21 @@ def convert_non_standard_amino_acids(sequence):
     return converted_sequence
 def do_alignment(identifier, uniprotSequence, pdbSequence, alignment_path):
     print(f'Aligning Datapoint: {identifier}')
-    print(pdbSequence)
-    print('uniprot Seq')
-    print(uniprotSequence)
-    #if len(pdbSequence) >= 1:
-    #f = open(Path(alignment_path / f'{identifier}_alignment.txt'),"w")
-    uniprotSequence = convert_non_standard_amino_acids(uniprotSequence) 
-    pdbSequence = convert_non_standard_amino_acids(pdbSequence) 
-    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')
-    print(aligner.align(uniprotSequence, pdbSequence))
-    alignments = aligner.align(uniprotSequence, pdbSequence)
-    alignments = (list(alignments))
-    alignment_list = []
-    for alignment in alignments:
-        #f.write(str(alignment))
-        #f.write('\n')
-        #f.write('\n')
-        alignment = (str(alignment).strip().split('\n'))
-        alignment = [''.join(['.' if m == ' ' else m for m in x]) for x in alignment]
-        alignment_list.append(alignment)
+    if len(pdbSequence) >= 1:
+        uniprotSequence = convert_non_standard_amino_acids(uniprotSequence) 
+        pdbSequence = convert_non_standard_amino_acids(pdbSequence) 
+        aligner.mode = 'local'
+        aligner.substitution_matrix = substitution_matrices.load("BLOSUM62")
+        aligner.open_gap_score = -11
+        aligner.extend_gap_score = -1
+        alignments = aligner.align(uniprotSequence, pdbSequence)
+        alignments = (list(alignments))
+        alignment_list = []
+        for alignment in alignments:
+            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')
     print(alignment_list)
     return alignment_list