Update code/add_alignment.py

code/add_alignment.py

@@ -11,22 +11,22 @@ def do_alignment(identifier, uniprotSequence, pdbSequence, alignment_path):
     print(pdbSequence)
     print('uniprot Seq')
     print(uniprotSequence)
-    if len(pdbSequence) >= 1:
-        #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
-        aligner.extend_gap_score = -1
-        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:
+    #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
+    aligner.extend_gap_score = -1
+    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)
     print(alignment_list)
     return alignment_list