Merge pull request #4415 from broadinstitute/show-all-consequence-terms

show all vep consequence terms
broadinstitute · Oct 10, 2024 · 80469a6 · 80469a6
2 parents 7deebf1 + 7f219ae
commit 80469a6
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Showing 5 changed files with 31 additions and 23 deletions.
diff --git a/hail_search/queries/mito.py b/hail_search/queries/mito.py
@@ -1,5 +1,3 @@
-from collections import defaultdict
-
 from aiohttp.web import HTTPNotFound
 import hail as hl
 import logging
@@ -96,7 +94,6 @@ class MitoHailTableQuery(BaseHailTableQuery):
         TRANSCRIPTS_FIELD: {
             **BaseHailTableQuery.ENUM_ANNOTATION_FIELDS['transcripts'],
             'annotate_value': lambda transcript, *args: {'major_consequence': transcript.consequence_terms.first()},
-            'drop_fields': ['consequence_terms'],
             'format_array_values': lambda values, *args: BaseHailTableQuery.ENUM_ANNOTATION_FIELDS['transcripts']['format_array_values'](values).map_values(
                 lambda transcripts: hl.enumerate(transcripts).starmap(lambda i, t: t.annotate(transcriptRank=i))
             ),

diff --git a/hail_search/test_search.py b/hail_search/test_search.py
@@ -107,14 +107,15 @@
         'ENSG00000271079': [
             {'aminoAcids': 'E/G', 'canonical': 1, 'codons': 'gAa/gGa', 'geneId': 'ENSG00000271079',
              'hgvsc': 'ENST00000420911.2:c.1262A>G', 'hgvsp': 'ENSP00000474204.1:p.Glu421Gly',
-             'transcriptId': 'ENST00000420911', 'isLofNagnag': None, 'transcriptRank': 0,
+             'transcriptId': 'ENST00000420911', 'isLofNagnag': None, 'transcriptRank': 0, 'consequenceTerms': ['missense_variant'],
              'biotype': 'protein_coding', 'lofFilters': None, 'majorConsequence': 'missense_variant'},
         ],
         'ENSG00000176227': [
             {'aminoAcids': None, 'canonical': 1, 'codons': None, 'geneId': 'ENSG00000176227',
              'hgvsc': 'ENST00000447022.1:n.1354A>G', 'hgvsp': None,
              'transcriptId': 'ENST00000447022', 'isLofNagnag': None, 'transcriptRank': 0,
-             'biotype': 'processed_pseudogene', 'lofFilters': None, 'majorConsequence': 'non_coding_transcript_exon_variant'},
+             'biotype': 'processed_pseudogene', 'lofFilters': None, 'majorConsequence': 'non_coding_transcript_exon_variant',
+             'consequenceTerms': ['non_coding_transcript_exon_variant', 'non_coding_transcript_variant']},
         ],
     },
     'mainTranscriptId': 'ENST00000420911',