Merge pull request #9 from briney/development

fixed D-gene assignment bug
brineylab · Feb 20, 2016 · 201a6b1 · 201a6b1
2 parents b54e789 + a7b33a8
commit 201a6b1
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Showing 3 changed files with 10 additions and 5 deletions.
diff --git a/abstar/abstar.py b/abstar/abstar.py
@@ -433,10 +433,11 @@ def _run_jobs_singlethreaded(files, output_dir, args):
     for i, f in enumerate(files):
         try:
             results.append(run_vdj(f, output_dir, args))
-            update_progress(i, len(files))
+            update_progress(i + 1, len(files))
         except:
             logger.debug('FILE-LEVEL EXCEPTION: {}'.format(f))
             logging.debug(traceback.format_exc())
+    logger.info('')
     return results
 
 

diff --git a/abstar/utils/output.py b/abstar/utils/output.py
@@ -333,7 +333,7 @@ def _imgt_summary_output(vdj, header=False):
             ('J-REGION score', vdj.j.top_score),
             ('J-REGION identity %', round(vdj.j.nt_mutations.germline_identity, 2)),
             ('J-REGION identity nt', _get_iden_nt(vdj.j)),
-            ('D-GENE and allele', vdj.d.top_germline if vdj.d else ''),
+            ('D-GENE and allele', vdj.d.top_germline if vdj.d is not None else ''),
             ('D-REGION reading frame', vdj.d.reading_frame if vdj.d else ''),
             ('CDR1-IMGT length', vdj.v.regions.aa_lengths['CDR1']),
             ('CDR2-IMGT length', vdj.v.regions.aa_lengths['CDR2']),

diff --git a/abstar/utils/vdj.py b/abstar/utils/vdj.py
@@ -415,10 +415,11 @@ def process_sequence_file(seq_file, args):
             if v.chain == 'heavy':
                 junc_start = len(v.query_alignment) + v.query_start
                 junc_end = junc_start + j.query_start
-                junction = Sequence(seq.id, seq.sequence[junc_start:junc_end])
+                junction = Sequence(seq.sequence[junc_start:junc_end], id=seq.id)
                 if junction:
                     d = assign_d(junction, args.species)
-                    logger.debug('ASSIGNED D-GENE: {}, {}'.format(seq.id, d.top_germline))
+                    if d is not None:
+                    	logger.debug('ASSIGNED D-GENE: {}, {}'.format(seq.id, d.top_germline))
                     vdjs.append(VDJ(seq, args, v, j, d))
                     continue
                 vdjs.append(VDJ(seq, args, v, j))
@@ -466,4 +467,7 @@ def assign_d(seq, species):
     alignments = local_alignment(seq, targets=germs,
                                  gap_open_penalty=20, gap_extend_penalty=2)
     alignments.sort(key=lambda x: x.score, reverse=True)
-    return blast.DiversityResult(seq, alignments[:5])
+    try:
+    	return blast.DiversityResult(seq, alignments[:5])
+    except IndexError:
+    	return None