Merge pull request #100 from phac-nml/fix/98-mixed-subtype

Fix #98 QC check for mixed subtypes

bio_hansel/qc/checks.py

@@ -140,7 +140,7 @@ def is_mixed_subtype(st: Subtype, df: pd.DataFrame, *args) -> Tuple[Optional[str
     """
     if not st.are_subtypes_consistent:
         return QC.FAIL, f'Mixed subtypes found: "{"; ".join(sorted(st.inconsistent_subtypes))}".'
-    conflicting_kmers = get_conflicting_kmers(st, df)
+    conflicting_kmers = get_conflicting_kmers(st.subtype, df, st.is_fastq_input())
     if conflicting_kmers is None or conflicting_kmers.shape[0] == 0:
         return None, None
 
@@ -250,7 +250,7 @@ def is_maybe_intermediate_subtype(st: Subtype, df: pd.DataFrame, p: SubtypingPar
 
     total_subtype_kmers = int(st.n_kmers_matching_subtype_expected)
     total_subtype_kmers_hits = int(st.n_kmers_matching_subtype)
-    conflicting_kmers = get_conflicting_kmers(st, df)
+    conflicting_kmers = get_conflicting_kmers(st.subtype, df, st.is_fastq_input())
     num_pos_kmers, num_neg_kmers = get_num_pos_neg_kmers(st, df)
     obs = int(st.n_kmers_matching_all)
     exp = int(st.n_kmers_matching_all_expected)

bio_hansel/qc/utils.py

@@ -1,11 +1,25 @@
-from typing import Tuple, Optional, List, Any, Dict
+from typing import Tuple, Optional, List, Any, Dict, Iterable
 
 from pandas import DataFrame
 
 from ..subtype import Subtype
 
 
-def get_conflicting_kmers(st: Subtype, df: DataFrame) -> Optional[DataFrame]:
+def component_subtypes(subtype: str) -> Iterable[str]:
+    """Generate component subtypes from a subtype.
+
+    Args:
+        subtype: Subtype string, e.g. "4.2.1.1"
+    Yields:
+        Component subtypes (e.g. for subtype "4.2.1.1", will yield
+        ['4', '4.2', '4.2.1', '4.2.1.1'])
+    """
+    split_subtype = subtype.split('.')
+    for i, x in enumerate(split_subtype):
+        yield '.'.join(split_subtype[:i+1])
+
+
+def get_conflicting_kmers(subtype: str, df: DataFrame, is_fastq_input: bool = True) -> Optional[DataFrame]:
     """ Get positive and negative kmers that both are present for a subtype.
 
     Find positive and negative kmers for the same refposition/target site in the results `df`.
@@ -17,10 +31,9 @@ def get_conflicting_kmers(st: Subtype, df: DataFrame) -> Optional[DataFrame]:
     Returns:
         DataFrame of conflicting positive and negative kmers
     """
-    if st.is_fastq_input():
-        dfst = df[(df['subtype'] == str(st.subtype)) & (df['is_kmer_freq_okay'])]
-    else:  # fasta files
-        dfst = df[(df['subtype'] == str(st.subtype))]
+    dfst = df[(df['subtype'].isin(list(component_subtypes(subtype))))]
+    if is_fastq_input:
+        dfst = dfst[dfst['is_kmer_freq_okay']]
 
     pos_kmer_positions = dfst[dfst['is_pos_kmer']]['refposition']
     neg_kmers = dfst[~dfst['is_pos_kmer']]

tests/data/qc/conflicting_subtypes/fail.tsv

@@ -0,0 +1,64 @@
+refposition	subtype	is_pos_kmer	is_kmer_freq_okay
+931123	4	True	True
+62657	4.1	True	True
+891756	4.1.2	True	True
+3216553	1.1.1.1	False	True
+3479545	1.2.1	False	True
+3470377	1.2.2	False	True
+3466426	4.6	False	True
+3388166	4.3.2.1	False	True
+3273107	3	False	True
+3021283	1.1.1	False	True
+3722702	3.1.2	False	True
+2875883	4.6.2.2	False	True
+2874344	3.1.2.2	False	True
+2831482	8.1	False	True
+2694560	4.4.1.2	False	True
+2622402	1.1.2	False	True
+3570528	4.6.2.1	False	True
+62657	4.1	False	True
+2411730	4.2	False	True
+3836274	2.2.1.2	False	True
+3836739	4.8	False	True
+3977226	4.3.4	False	True
+4125058	4.6.2	False	True
+4151558	4.4.1	False	True
+4229087	4.1.1.3	False	True
+4246508	4.4.2	False	True
+4248115	2.2.1.1	False	True
+4249732	4.7	False	True
+4260268	4.6.1	False	True
+4307886	4.4	False	True
+4316114	4.3.2	False	True
+4398141	4.3.4.1	False	True
+2505085	2.2	False	True
+1881090	2.1	False	True
+1882180	8	False	True
+874787	4.6.1.1	False	True
+107794	4.1.2.1	False	True
+346693	2.2.2	False	True
+355181	4.4.1.1	False	True
+403364	4.3.3	False	True
+497491	2	False	True
+514245	4.1.1	False	True
+541048	4.1.1.2	False	True
+615614	4.3.1	False	True
+615938	1	False	True
+764995	4.3	False	True
+783601	4.2.1	False	True
+797736	2.2.1	False	True
+1084911	3.1.1	False	True
+1850119	4.1.1.1	False	True
+1132368	4.3.4.2	False	True
+1137518	7	False	True
+1237818	3.1.2.1	False	True
+1455780	4.2.2.1	False	True
+1487796	4.2.2	False	True
+1491275	1.1.3	False	True
+1501468	4.6.1.2	False	True
+1502120	4.3.4.2.1	False	True
+1719757	4.5	False	True
+1759252	4.9	False	True
+1799921	5	False	True
+1816587	8.2	False	True
+4404247	1.1	False	True

tests/data/qc/conflicting_subtypes/pass.tsv

@@ -0,0 +1,63 @@
+refposition	subtype	is_pos_kmer	is_kmer_freq_okay
+931123	4	True	True
+62657	4.1	True	True
+891756	4.1.2	True	True
+3216553	1.1.1.1	False	True
+3479545	1.2.1	False	True
+3470377	1.2.2	False	True
+3466426	4.6	False	True
+3388166	4.3.2.1	False	True
+3273107	3	False	True
+3021283	1.1.1	False	True
+3722702	3.1.2	False	True
+2875883	4.6.2.2	False	True
+2874344	3.1.2.2	False	True
+2831482	8.1	False	True
+2694560	4.4.1.2	False	True
+2622402	1.1.2	False	True
+3570528	4.6.2.1	False	True
+2411730	4.2	False	True
+3836274	2.2.1.2	False	True
+3836739	4.8	False	True
+3977226	4.3.4	False	True
+4125058	4.6.2	False	True
+4151558	4.4.1	False	True
+4229087	4.1.1.3	False	True
+4246508	4.4.2	False	True
+4248115	2.2.1.1	False	True
+4249732	4.7	False	True
+4260268	4.6.1	False	True
+4307886	4.4	False	True
+4316114	4.3.2	False	True
+4398141	4.3.4.1	False	True
+2505085	2.2	False	True
+1881090	2.1	False	True
+1882180	8	False	True
+874787	4.6.1.1	False	True
+107794	4.1.2.1	False	True
+346693	2.2.2	False	True
+355181	4.4.1.1	False	True
+403364	4.3.3	False	True
+497491	2	False	True
+514245	4.1.1	False	True
+541048	4.1.1.2	False	True
+615614	4.3.1	False	True
+615938	1	False	True
+764995	4.3	False	True
+783601	4.2.1	False	True
+797736	2.2.1	False	True
+1084911	3.1.1	False	True
+1850119	4.1.1.1	False	True
+1132368	4.3.4.2	False	True
+1137518	7	False	True
+1237818	3.1.2.1	False	True
+1455780	4.2.2.1	False	True
+1487796	4.2.2	False	True
+1491275	1.1.3	False	True
+1501468	4.6.1.2	False	True
+1502120	4.3.4.2.1	False	True
+1719757	4.5	False	True
+1759252	4.9	False	True
+1799921	5	False	True
+1816587	8.2	False	True
+4404247	1.1	False	True

tests/test_qc_utils.py

@@ -2,7 +2,12 @@
 
 import pandas as pd
 
-from bio_hansel.qc.utils import get_mixed_subtype_kmer_counts
+
+from bio_hansel.qc.utils import get_mixed_subtype_kmer_counts, component_subtypes, get_conflicting_kmers
+
+
+fail_tsv = 'tests/data/qc/conflicting_subtypes/fail.tsv'
+pass_tsv = 'tests/data/qc/conflicting_subtypes/pass.tsv'
 
 
 def test_get_mixed_subtype_kmer_counts():
@@ -22,3 +27,21 @@ def test_get_mixed_subtype_kmer_counts():
     assert(int(st_pos_kmers.get('2.1')) == 5)
     assert(int(st_pos_kmers.get('2.2')) == 3)
     assert(int(st_pos_kmers.get('0')) == 1)
+
+
+def test_component_subtypes():
+    assert list(component_subtypes('4.2.1.1')) == ['4', '4.2', '4.2.1', '4.2.1.1']
+    assert list(component_subtypes('1')) == ['1']
+
+
+def test_get_conflicting_kmers():
+    df_pass = pd.read_csv(pass_tsv, sep='\t')
+    df_pass_result = get_conflicting_kmers('4.1.2', df_pass, True)
+    assert df_pass_result.shape[0] == 0, 'Must be no conflicting kmers'
+    df_fail = pd.read_csv(fail_tsv, sep='\t')
+    df_fail_result = get_conflicting_kmers('4.1.2', df_fail, True)
+    df_fail_result.reset_index(inplace=True)
+    assert df_fail_result.shape[0] == 1, 'Must be one conflicting kmer'
+    assert df_fail_result.refposition[0] == 62657
+    assert df_fail_result.subtype[0] == '4.1'
+    assert df_fail_result.is_pos_kmer[0] == False