Fix summarizeFasta that summarize table keys not determined correctly with source comb in --order-source

moPepGen/aa/PeptidePoolSummarizer.py

@@ -303,7 +303,8 @@ def write_summary_table(self, handle:IO):
         summary_keys = self.summary_table.get_keys()
         header = '\t'.join(['sources', *summary_keys])
         handle.write(header + '\n')
-        sources = [it[0] for it in sorted(self.order.items(), key=lambda x:x[1])]
+        sources = [it[0] for it in sorted(self.order.items(), key=lambda x:x[1])
+                    if not isinstance(it[0], frozenset)]
         for i in range(len(sources)):
             for comb in itertools.combinations(sources, i + 1):
                 if self.ignore_missing_source:

test/unit/test_peptide_pool_summarizer.py

@@ -0,0 +1,81 @@
+""" Module for testing PeptidePoolSummarizer """
+import copy
+import io
+from contextlib import redirect_stdout
+import unittest
+from test.unit import create_aa_record, create_genomic_annotation, get_tx2gene_and_coding_tx
+from test.unit.test_peptide_pool_splitter import (
+    LABEL_MAP1, SOURCE_ORDER, ANNOTATION_DATA,
+)
+from moPepGen.aa.PeptidePoolSummarizer import PeptidePoolSummarizer
+from moPepGen.aa.PeptidePoolSplitter import LabelSourceMapping
+from moPepGen.aa import VariantPeptidePool
+
+
+SOURCE_PARSER_MAP = {
+    'gSNP': 'parseVEP',
+    'gINDEL': 'parseVEP',
+    'sSNV': 'parseVEP',
+    'sINDEL': 'parseVEP',
+    'altSplice': 'parseRMATS',
+    'Fusion': 'parseSTARFusion',
+    'circRNA': 'parseCIRCExplorer'
+}
+
+class TestPeptidePoolSummarizer(unittest.TestCase):
+    """ Test cases for PeptidePoolSummarizer """
+    def test_summarize_fasta_case1(self):
+        """ basic test """
+        anno = create_genomic_annotation(ANNOTATION_DATA)
+        tx2gene, coding_tx = get_tx2gene_and_coding_tx(anno)
+        peptides_data = [[ 'SSSSSSSR', 'ENST0001|SNV-1001-T-A|1' ]]
+        peptides = VariantPeptidePool({create_aa_record(*x) for x in peptides_data})
+        label_map = LabelSourceMapping(copy.copy(LABEL_MAP1))
+        summarizer = PeptidePoolSummarizer(
+            peptides, order=copy.copy(SOURCE_ORDER), label_map=label_map,
+        )
+        summarizer.count_peptide_source(
+            tx2gene=tx2gene,
+            coding_tx=coding_tx,
+            enzyme='trypsin'
+        )
+        self.assertEqual(set(summarizer.summary_table.data.keys()), {frozenset(['gSNP'])})
+
+    def test_summarize_fasta_source_comb_order(self):
+        """ When source combination is present in --order-source """
+        anno = create_genomic_annotation(ANNOTATION_DATA)
+        anno.transcripts['ENST0005'] = copy.deepcopy(anno.transcripts['ENST0002'])
+        anno.transcripts['ENST0005'].is_protein_coding = False
+        tx2gene, coding_tx = get_tx2gene_and_coding_tx(anno)
+        peptides_data = [
+            [
+                'SSSSSSSR',
+                'CIRC-ENST0002-E1-E2|1 ENST0005|SE-2100|1'
+            ]
+        ]
+        peptides = VariantPeptidePool({create_aa_record(*x) for x in peptides_data})
+        label_map = LabelSourceMapping(copy.copy(LABEL_MAP1))
+        # order = copy.copy(SOURCE_ORDER)
+        order = {
+            'altSplice': 1,
+            frozenset(['altSplice', 'Noncoding']): 2,
+            'Noncoding': 3,
+            'circRNA': 4
+        }
+        source_parser_map = copy.deepcopy(SOURCE_PARSER_MAP)
+        summarizer = PeptidePoolSummarizer(
+            peptides, order=order, label_map=label_map, source_parser_map=source_parser_map
+        )
+        summarizer.count_peptide_source(
+            tx2gene=tx2gene,
+            coding_tx=coding_tx,
+            enzyme='trypsin'
+        )
+        self.assertEqual(
+            set(summarizer.summary_table.data.keys()),
+            {frozenset(['altSplice', 'Noncoding'])}
+        )
+
+        handle = io.StringIO()
+        with redirect_stdout(handle):
+            summarizer.write_summary_table(handle)