diff --git a/hail_search/fixtures/GRCh38/MITO/annotations.ht/.README.txt.crc b/hail_search/fixtures/GRCh38/MITO/annotations.ht/.README.txt.crc index 4937f949de..943e1c4927 100644 Binary files a/hail_search/fixtures/GRCh38/MITO/annotations.ht/.README.txt.crc and b/hail_search/fixtures/GRCh38/MITO/annotations.ht/.README.txt.crc differ diff --git a/hail_search/fixtures/GRCh38/MITO/annotations.ht/.metadata.json.gz.crc b/hail_search/fixtures/GRCh38/MITO/annotations.ht/.metadata.json.gz.crc index 679f60ca2c..d84fab48ff 100644 Binary files a/hail_search/fixtures/GRCh38/MITO/annotations.ht/.metadata.json.gz.crc and b/hail_search/fixtures/GRCh38/MITO/annotations.ht/.metadata.json.gz.crc differ diff --git a/hail_search/fixtures/GRCh38/MITO/annotations.ht/README.txt b/hail_search/fixtures/GRCh38/MITO/annotations.ht/README.txt index c1f060502b..68d42eca18 100644 --- a/hail_search/fixtures/GRCh38/MITO/annotations.ht/README.txt +++ b/hail_search/fixtures/GRCh38/MITO/annotations.ht/README.txt @@ -1,3 +1,3 @@ This folder comprises a Hail (www.hail.is) native Table or MatrixTable. Written with version 0.2.128-eead8100a1c1 - Created at 2024/02/26 14:35:40 \ No newline at end of file + Created at 2024/10/14 16:14:00 \ No newline at end of file diff --git a/hail_search/fixtures/GRCh38/MITO/annotations.ht/index/part-0-636edbd3-d0a9-410f-b5fe-03749bbbd8db.idx/.index.crc b/hail_search/fixtures/GRCh38/MITO/annotations.ht/index/part-0-636edbd3-d0a9-410f-b5fe-03749bbbd8db.idx/.index.crc new file mode 100644 index 0000000000..60ec208eaa Binary files /dev/null and b/hail_search/fixtures/GRCh38/MITO/annotations.ht/index/part-0-636edbd3-d0a9-410f-b5fe-03749bbbd8db.idx/.index.crc differ diff --git a/hail_search/fixtures/GRCh38/MITO/annotations.ht/index/part-0-9051c447-510b-49ab-bf6a-cadcf5f69801.idx/.metadata.json.gz.crc b/hail_search/fixtures/GRCh38/MITO/annotations.ht/index/part-0-636edbd3-d0a9-410f-b5fe-03749bbbd8db.idx/.metadata.json.gz.crc similarity index 100% rename from hail_search/fixtures/GRCh38/MITO/annotations.ht/index/part-0-9051c447-510b-49ab-bf6a-cadcf5f69801.idx/.metadata.json.gz.crc rename to hail_search/fixtures/GRCh38/MITO/annotations.ht/index/part-0-636edbd3-d0a9-410f-b5fe-03749bbbd8db.idx/.metadata.json.gz.crc diff --git a/hail_search/fixtures/GRCh38/MITO/annotations.ht/index/part-0-636edbd3-d0a9-410f-b5fe-03749bbbd8db.idx/index b/hail_search/fixtures/GRCh38/MITO/annotations.ht/index/part-0-636edbd3-d0a9-410f-b5fe-03749bbbd8db.idx/index new file mode 100644 index 0000000000..b5e11439a9 Binary files /dev/null and b/hail_search/fixtures/GRCh38/MITO/annotations.ht/index/part-0-636edbd3-d0a9-410f-b5fe-03749bbbd8db.idx/index differ diff --git a/hail_search/fixtures/GRCh38/MITO/annotations.ht/index/part-0-9051c447-510b-49ab-bf6a-cadcf5f69801.idx/metadata.json.gz b/hail_search/fixtures/GRCh38/MITO/annotations.ht/index/part-0-636edbd3-d0a9-410f-b5fe-03749bbbd8db.idx/metadata.json.gz similarity index 100% rename from hail_search/fixtures/GRCh38/MITO/annotations.ht/index/part-0-9051c447-510b-49ab-bf6a-cadcf5f69801.idx/metadata.json.gz rename to hail_search/fixtures/GRCh38/MITO/annotations.ht/index/part-0-636edbd3-d0a9-410f-b5fe-03749bbbd8db.idx/metadata.json.gz diff --git a/hail_search/fixtures/GRCh38/MITO/annotations.ht/index/part-0-9051c447-510b-49ab-bf6a-cadcf5f69801.idx/.index.crc b/hail_search/fixtures/GRCh38/MITO/annotations.ht/index/part-0-9051c447-510b-49ab-bf6a-cadcf5f69801.idx/.index.crc deleted file mode 100644 index 28fd510852..0000000000 Binary files a/hail_search/fixtures/GRCh38/MITO/annotations.ht/index/part-0-9051c447-510b-49ab-bf6a-cadcf5f69801.idx/.index.crc and /dev/null differ diff --git a/hail_search/fixtures/GRCh38/MITO/annotations.ht/index/part-0-9051c447-510b-49ab-bf6a-cadcf5f69801.idx/index b/hail_search/fixtures/GRCh38/MITO/annotations.ht/index/part-0-9051c447-510b-49ab-bf6a-cadcf5f69801.idx/index deleted file mode 100644 index 5e9bf53815..0000000000 Binary files a/hail_search/fixtures/GRCh38/MITO/annotations.ht/index/part-0-9051c447-510b-49ab-bf6a-cadcf5f69801.idx/index and /dev/null differ diff --git a/hail_search/fixtures/GRCh38/MITO/annotations.ht/metadata.json.gz b/hail_search/fixtures/GRCh38/MITO/annotations.ht/metadata.json.gz index 053455974f..d5ab0c21f4 100644 Binary files a/hail_search/fixtures/GRCh38/MITO/annotations.ht/metadata.json.gz and b/hail_search/fixtures/GRCh38/MITO/annotations.ht/metadata.json.gz differ diff --git a/hail_search/fixtures/GRCh38/MITO/annotations.ht/rows/.metadata.json.gz.crc b/hail_search/fixtures/GRCh38/MITO/annotations.ht/rows/.metadata.json.gz.crc index 30cea52086..20b8c4ec1b 100644 Binary files a/hail_search/fixtures/GRCh38/MITO/annotations.ht/rows/.metadata.json.gz.crc and b/hail_search/fixtures/GRCh38/MITO/annotations.ht/rows/.metadata.json.gz.crc differ diff --git a/hail_search/fixtures/GRCh38/MITO/annotations.ht/rows/metadata.json.gz b/hail_search/fixtures/GRCh38/MITO/annotations.ht/rows/metadata.json.gz index 209fd4124b..ce71f9506d 100644 Binary files a/hail_search/fixtures/GRCh38/MITO/annotations.ht/rows/metadata.json.gz and b/hail_search/fixtures/GRCh38/MITO/annotations.ht/rows/metadata.json.gz differ diff --git a/hail_search/fixtures/GRCh38/MITO/annotations.ht/rows/parts/.part-0-636edbd3-d0a9-410f-b5fe-03749bbbd8db.crc b/hail_search/fixtures/GRCh38/MITO/annotations.ht/rows/parts/.part-0-636edbd3-d0a9-410f-b5fe-03749bbbd8db.crc new file mode 100644 index 0000000000..d4ffb8e8ab Binary files /dev/null and b/hail_search/fixtures/GRCh38/MITO/annotations.ht/rows/parts/.part-0-636edbd3-d0a9-410f-b5fe-03749bbbd8db.crc differ diff --git a/hail_search/fixtures/GRCh38/MITO/annotations.ht/rows/parts/.part-0-9051c447-510b-49ab-bf6a-cadcf5f69801.crc b/hail_search/fixtures/GRCh38/MITO/annotations.ht/rows/parts/.part-0-9051c447-510b-49ab-bf6a-cadcf5f69801.crc deleted file mode 100644 index 372cf56ea1..0000000000 Binary files a/hail_search/fixtures/GRCh38/MITO/annotations.ht/rows/parts/.part-0-9051c447-510b-49ab-bf6a-cadcf5f69801.crc and /dev/null differ diff --git a/hail_search/fixtures/GRCh38/MITO/annotations.ht/rows/parts/part-0-636edbd3-d0a9-410f-b5fe-03749bbbd8db b/hail_search/fixtures/GRCh38/MITO/annotations.ht/rows/parts/part-0-636edbd3-d0a9-410f-b5fe-03749bbbd8db new file mode 100644 index 0000000000..af69270757 Binary files /dev/null and b/hail_search/fixtures/GRCh38/MITO/annotations.ht/rows/parts/part-0-636edbd3-d0a9-410f-b5fe-03749bbbd8db differ diff --git a/hail_search/fixtures/GRCh38/MITO/annotations.ht/rows/parts/part-0-9051c447-510b-49ab-bf6a-cadcf5f69801 b/hail_search/fixtures/GRCh38/MITO/annotations.ht/rows/parts/part-0-9051c447-510b-49ab-bf6a-cadcf5f69801 deleted file mode 100644 index 1c587b0747..0000000000 Binary files a/hail_search/fixtures/GRCh38/MITO/annotations.ht/rows/parts/part-0-9051c447-510b-49ab-bf6a-cadcf5f69801 and /dev/null differ diff --git a/hail_search/queries/mito.py b/hail_search/queries/mito.py index b5cd274515..6b46ada427 100644 --- a/hail_search/queries/mito.py +++ b/hail_search/queries/mito.py @@ -59,6 +59,7 @@ class MitoHailTableQuery(BaseHailTableQuery): 'mitotip': PredictionPath('mitotip', 'trna_prediction'), 'mut_taster': PredictionPath('dbnsfp_mito', 'MutationTaster_pred'), 'sift': PredictionPath('dbnsfp_mito', 'SIFT_score'), + 'mlc': PredictionPath('local_constraint_mito', 'score'), } PATHOGENICITY_FILTERS = { diff --git a/hail_search/test_utils.py b/hail_search/test_utils.py index e7dc290552..6895b8df25 100644 --- a/hail_search/test_utils.py +++ b/hail_search/test_utils.py @@ -849,6 +849,7 @@ 'mitotip': 'likely_pathogenic', 'mut_taster': None, 'sift': None, + 'mlc': 3.38874, }, 'commonLowHeteroplasmy': False, 'highConstraintRegion': True, @@ -902,6 +903,7 @@ 'mitotip': None, 'mut_taster': 'N', 'sift': 0, + 'mlc': None, }, 'commonLowHeteroplasmy': False, 'highConstraintRegion': True, @@ -948,6 +950,7 @@ 'mitotip': None, 'mut_taster': None, 'sift': None, + 'mlc': 0.7514, }, 'commonLowHeteroplasmy': True, 'highConstraintRegion': False, diff --git a/ui/shared/utils/constants.js b/ui/shared/utils/constants.js index a757d9570c..54f7fc72a3 100644 --- a/ui/shared/utils/constants.js +++ b/ui/shared/utils/constants.js @@ -1515,6 +1515,7 @@ export const ORDERED_PREDICTOR_FIELDS = [ { field: 'haplogroup_defining', indicatorMap: { Y: { color: 'green', value: '' } } }, { field: 'mitotip', indicatorMap: MITOTIP_MAP, fieldTitle: 'MitoTIP' }, { field: 'hmtvar', thresholds: [undefined, undefined, 0.35, 0.35, undefined], fieldTitle: 'HmtVar' }, + { field: 'mlc', thresholds: [undefined, 0.5, 0.5, 0.75, undefined], fieldTitle: 'MLC' }, ] export const coloredIcon = color => React.createElement(color.startsWith('#') ? ColoredIcon : Icon, { name: 'circle', size: 'small', color })