Fix #470 by overriding MIDI subtypes based on main sample's subtype.

cfe-lab · Jun 18, 2019 · 607acfa · 607acfa
1 parent ee8e707
commit 607acfa
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Showing 2 changed files with 44 additions and 7 deletions.
diff --git a/micall/resistance/resistance.py b/micall/resistance/resistance.py
@@ -143,9 +143,9 @@ def combine_aminos(amino_csv, midi_amino_csv, failures):
             except LowCoverageError as ex:
                 failures[(seed, region, is_midi)] = ex.args[0]
                 continue
-            midi_rows[seed] = [row
-                               for row in rows
-                               if 226 < int(row['refseq.aa.pos'])]
+            midi_rows[get_genotype(seed)] = [row
+                                             for row in rows
+                                             if 226 < int(row['refseq.aa.pos'])]
     is_midi = False
     for (seed, region), rows in groupby(DictReader(amino_csv),
                                         itemgetter('seed', 'region')):
@@ -157,7 +157,8 @@ def combine_aminos(amino_csv, midi_amino_csv, failures):
             main_rows = []
             low_coverage_message = ex.args[0]
         if region.endswith('-NS5b'):
-            region_midi_rows = midi_rows.pop(seed, None)
+            genotype = get_genotype(seed)
+            region_midi_rows = midi_rows.pop(genotype, None)
             if region_midi_rows is None:
                 region_midi_rows = all_rows
                 if is_midi_separate:
@@ -171,14 +172,15 @@ def combine_aminos(amino_csv, midi_amino_csv, failures):
                     low_coverage_message = None
                 except LowCoverageError:
                     region_midi_rows = []
-            main_rows = combine_midi_rows(main_rows, region_midi_rows)
+            main_rows = combine_midi_rows(main_rows, region_midi_rows, seed)
         if low_coverage_message:
             failures[(seed, region, is_midi)] = low_coverage_message
         yield from main_rows
 
     # Check for MIDI regions that had no match.
-    for seed, rows in sorted(midi_rows.items()):
+    for genotype, rows in sorted(midi_rows.items()):
         region = rows[0]['region']
+        seed = rows[0]['seed']
         failures.setdefault((seed, region, False), NOTHING_MAPPED_MESSAGE)
         yield from rows
 
@@ -193,7 +195,7 @@ def write_failure(fail_writer, seed, region, reason):
                               reason=reason))
 
 
-def combine_midi_rows(main_rows, midi_rows):
+def combine_midi_rows(main_rows, midi_rows, seed):
     main_row_map = {int(row['refseq.aa.pos']): row
                     for row in main_rows}
     midi_row_map = {int(row['refseq.aa.pos']): row
@@ -208,6 +210,7 @@ def combine_midi_rows(main_rows, midi_rows):
             if pos <= 336:
                 yield main_row
         elif main_row is None:
+            midi_row['seed'] = seed  # Override MIDI seed with main seed.
             yield midi_row
         elif (pos <= 336 and
               int(main_row['coverage']) > int(midi_row['coverage'])):

diff --git a/micall/tests/test_resistance.py b/micall/tests/test_resistance.py
@@ -309,6 +309,40 @@ def test_combine_aminos_ns5b_multiple_seeds():
     check_combination(amino_csv, midi_amino_csv, expected_csv, expected_failures)
 
 
+def test_combine_aminos_ns5b_multiple_subtypes():
+    """ Main sample's subtype overrides MIDI subtype when they disagree. """
+    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-4c,HCV4-ED43-NS5b,15,1,1,0,0,0,0,0,0,0,0,10000,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,10000
+HCV-4c,HCV4-ED43-NS5b,15,4,2,0,0,0,0,10000,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,10000
+HCV-4c,HCV4-ED43-NS5b,15,7,228,10000,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,10000
+""")
+    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-4m,HCV4-ED43-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-4m,HCV4-ED43-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-4m,HCV4-ED43-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-4m,HCV4-ED43-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
+""")
+    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-4c,HCV4-ED43-NS5b,15,1,1,0,0,0,0,0,0,0,0,10000,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,10000
+HCV-4c,HCV4-ED43-NS5b,15,4,2,0,0,0,0,10000,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,10000
+HCV-4c,HCV4-ED43-NS5b,15,7,228,10000,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,10000
+HCV-4c,HCV4-ED43-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-4c,HCV4-ED43-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-4c,HCV4-ED43-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-4c,HCV4-ED43-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
+"""
+
+    check_combination(amino_csv, midi_amino_csv, expected_csv)
+
+
 def test_combine_aminos_low_coverage_in_midi():
     amino_csv = StringIO("""\
 seed,region,q-cutoff,query.nuc.pos,refseq.aa.pos,\