Fix #462 by including unmatched MIDI samples.

micall/resistance/resistance.py

@@ -153,7 +153,7 @@ def combine_aminos(amino_csv, midi_amino_csv, failures):
             failures[(seed, region, is_midi)] = ex.args[0]
             rows = []
         if region.endswith('-NS5b'):
-            region_midi_rows = midi_rows.get(seed)
+            region_midi_rows = midi_rows.pop(seed, None)
             if region_midi_rows is None:
                 if is_midi_separate:
                     failures.setdefault((seed, region, True),
@@ -162,6 +162,12 @@ def combine_aminos(amino_csv, midi_amino_csv, failures):
             rows = combine_midi_rows(rows, region_midi_rows)
         yield from rows
 
+    # Check for MIDI regions that had no match.
+    for seed, rows in sorted(midi_rows.items()):
+        region = rows[0]['region']
+        failures.setdefault((seed, region, False), NOTHING_MAPPED_MESSAGE)
+        yield from rows
+
 
 def write_failure(fail_writer, seed, region, reason):
     reported_region = get_reported_region(region)

micall/tests/test_resistance.py

@@ -278,9 +278,14 @@ def test_combine_ns5b_multiple_seeds(self):
 HCV-1a,HCV1A-H77-NS5b,15,1,559,0,0,0,0,0,0,0,0,10000,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,10000
 HCV-1a,HCV1A-H77-NS5b,15,4,560,0,0,0,0,10000,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,10000
 HCV-1a,HCV1A-H77-NS5b,15,7,561,10000,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,10000
+HCV-1b,HCV1B-Con1-NS5b,15,1,558,0,0,0,0,0,0,0,0,20000,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,20000
+HCV-1b,HCV1B-Con1-NS5b,15,1,559,0,0,0,0,0,0,0,0,20000,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,20000
+HCV-1b,HCV1B-Con1-NS5b,15,4,560,0,0,0,0,20000,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,20000
+HCV-1b,HCV1B-Con1-NS5b,15,7,561,20000,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,20000
 """
+        expected_failures = {('HCV-1b', 'HCV1B-Con1-NS5b', False): 'nothing mapped'}
 
-        self.check_combination(amino_csv, midi_amino_csv, expected_csv)
+        self.check_combination(amino_csv, midi_amino_csv, expected_csv, expected_failures)
 
     def test_low_coverage_in_midi(self):
         amino_csv = StringIO("""\
@@ -336,6 +341,33 @@ def test_no_coverage_in_midi(self):
 
         self.check_combination(amino_csv, midi_amino_csv, expected_csv, expected_failures)
 
+    def test_no_coverage_in_ns5b(self):
+        amino_csv = StringIO("""\
+seed,region,q-cutoff,query.nuc.pos,refseq.aa.pos,\
+A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap,coverage
+""")
+        amino_csv.name = 'main_amino.csv'
+        midi_amino_csv = StringIO("""\
+seed,region,q-cutoff,query.nuc.pos,refseq.aa.pos,\
+A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap,coverage
+HCV-1a,HCV1A-H77-NS5b,15,1,558,0,0,0,0,0,0,0,0,10000,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,10000
+HCV-1a,HCV1A-H77-NS5b,15,1,559,0,0,0,0,0,0,0,0,10000,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,10000
+HCV-1a,HCV1A-H77-NS5b,15,4,560,0,0,0,0,10000,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,10000
+HCV-1a,HCV1A-H77-NS5b,15,7,561,10000,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,10000
+""")
+        midi_amino_csv.name = 'midi_amino.csv'
+        expected_csv = """\
+seed,region,q-cutoff,query.nuc.pos,refseq.aa.pos,\
+A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap,coverage
+HCV-1a,HCV1A-H77-NS5b,15,1,558,0,0,0,0,0,0,0,0,10000,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,10000
+HCV-1a,HCV1A-H77-NS5b,15,1,559,0,0,0,0,0,0,0,0,10000,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,10000
+HCV-1a,HCV1A-H77-NS5b,15,4,560,0,0,0,0,10000,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,10000
+HCV-1a,HCV1A-H77-NS5b,15,7,561,10000,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,10000
+"""
+        expected_failures = {('HCV-1a', 'HCV1A-H77-NS5b', False): 'nothing mapped'}
+
+        self.check_combination(amino_csv, midi_amino_csv, expected_csv, expected_failures)
+
     def test_midi_other_regions(self):
         amino_csv = StringIO("""\
 seed,region,q-cutoff,query.nuc.pos,refseq.aa.pos,\