From 4fc80a50e00719e62f9a9f014fe34c7cdcbec257 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Wed, 14 Feb 2024 14:45:55 -0500 Subject: [PATCH] fix tests --- hail_search/queries/sv.py | 2 +- hail_search/test_search.py | 6 +++--- seqr/utils/search/hail_search_utils_tests.py | 3 ++- 3 files changed, 6 insertions(+), 5 deletions(-) diff --git a/hail_search/queries/sv.py b/hail_search/queries/sv.py index aefbcdb6e9..d74939ae1b 100644 --- a/hail_search/queries/sv.py +++ b/hail_search/queries/sv.py @@ -80,7 +80,7 @@ def _filter_annotated_table(self, ht, *args, parsed_intervals=None, exclude_inte if padded_interval: padding = int((padded_interval['end'] - padded_interval['start']) * padded_interval['padding']) ht = ht.filter(hl.all([ - ht.start_locus.contig == padded_interval['chrom'], + ht.start_locus.contig == f"chr{padded_interval['chrom']}", self._locus_in_range(ht.start_locus, padded_interval['start'], padding), self._locus_in_range(ht.end_locus, padded_interval['end'], padding) ])) diff --git a/hail_search/test_search.py b/hail_search/test_search.py index d1e6967ee9..7fa714417d 100644 --- a/hail_search/test_search.py +++ b/hail_search/test_search.py @@ -612,17 +612,17 @@ async def test_location_search(self): ) await self._assert_expected_search( - [GCNV_VARIANT4], padded_interval={'chrom': '17', 'start': 38724781, 'end': 38738703, 'padding': 0.2}, + [GCNV_VARIANT4], padded_interval={'chrom': '17', 'start': 38720781, 'end': 38738703, 'padding': 0.2}, omit_sample_type='SNV_INDEL', ) await self._assert_expected_search( - [], padded_interval={'chrom': '17', 'start': 38722281, 'end': 38738703, 'padding': 0.1}, + [], padded_interval={'chrom': '17', 'start': 38720781, 'end': 38738703, 'padding': 0.1}, omit_sample_type='SNV_INDEL', ) await self._assert_expected_search( - [SV_VARIANT1], padded_interval={'chrom': '14', 'start': 106692244, 'end': 106742587, 'padding': 0.1}, + [SV_VARIANT4], padded_interval={'chrom': '14', 'start': 106692244, 'end': 106742587, 'padding': 0.1}, sample_data=SV_WGS_SAMPLE_DATA, ) diff --git a/seqr/utils/search/hail_search_utils_tests.py b/seqr/utils/search/hail_search_utils_tests.py index 3c72f4bb57..dfd25d662b 100644 --- a/seqr/utils/search/hail_search_utils_tests.py +++ b/seqr/utils/search/hail_search_utils_tests.py @@ -249,7 +249,8 @@ def test_variant_lookup(self): }) self._test_minimal_search_call(expected_search_body={ 'genome_version': 'GRCh38', 'data_type': 'SV_WES', 'annotations': {'structural': ['DEL', 'gCNV_DEL']}, - 'intervals': ['17:38718997-38738487'], 'sample_data': {'SV_WGS': SV_WGS_SAMPLE_DATA}, + 'padded_interval': {'chrom': '17', 'start': 38721781, 'end': 38735703, 'padding': 0.2}, + 'sample_data': {'SV_WGS': SV_WGS_SAMPLE_DATA}, }) # No second lookup call is made for non DELs/DUPs