Merge pull request #4426 from broadinstitute/mito-local-constraint

Mito local constraint
broadinstitute · Oct 15, 2024 · 01ff790 · 01ff790
2 parents afeb650 + 345d4d1
commit 01ff790
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diff --git a/hail_search/fixtures/GRCh38/MITO/annotations.ht/.README.txt.crc b/hail_search/fixtures/GRCh38/MITO/annotations.ht/.README.txt.crc
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
diff --git 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
+  Created at 2024/10/14 16:14:00
diff --git a/...Ch38/MITO/annotations.ht/index/part-0-636edbd3-d0a9-410f-b5fe-03749bbbd8db.idx/.index.crc b/...Ch38/MITO/annotations.ht/index/part-0-636edbd3-d0a9-410f-b5fe-03749bbbd8db.idx/.index.crc
diff --git a/...6a-cadcf5f69801.idx/.metadata.json.gz.crc → ...fe-03749bbbd8db.idx/.metadata.json.gz.crc b/...6a-cadcf5f69801.idx/.metadata.json.gz.crc → ...fe-03749bbbd8db.idx/.metadata.json.gz.crc
diff --git a/...es/GRCh38/MITO/annotations.ht/index/part-0-636edbd3-d0a9-410f-b5fe-03749bbbd8db.idx/index b/...es/GRCh38/MITO/annotations.ht/index/part-0-636edbd3-d0a9-410f-b5fe-03749bbbd8db.idx/index
diff --git a/...ab-bf6a-cadcf5f69801.idx/metadata.json.gz → ...0f-b5fe-03749bbbd8db.idx/metadata.json.gz b/...ab-bf6a-cadcf5f69801.idx/metadata.json.gz → ...0f-b5fe-03749bbbd8db.idx/metadata.json.gz
diff --git a/...Ch38/MITO/annotations.ht/index/part-0-9051c447-510b-49ab-bf6a-cadcf5f69801.idx/.index.crc b/...Ch38/MITO/annotations.ht/index/part-0-9051c447-510b-49ab-bf6a-cadcf5f69801.idx/.index.crc
diff --git a/...es/GRCh38/MITO/annotations.ht/index/part-0-9051c447-510b-49ab-bf6a-cadcf5f69801.idx/index b/...es/GRCh38/MITO/annotations.ht/index/part-0-9051c447-510b-49ab-bf6a-cadcf5f69801.idx/index
diff --git a/hail_search/fixtures/GRCh38/MITO/annotations.ht/metadata.json.gz b/hail_search/fixtures/GRCh38/MITO/annotations.ht/metadata.json.gz
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
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
diff --git a/...es/GRCh38/MITO/annotations.ht/rows/parts/.part-0-636edbd3-d0a9-410f-b5fe-03749bbbd8db.crc b/...es/GRCh38/MITO/annotations.ht/rows/parts/.part-0-636edbd3-d0a9-410f-b5fe-03749bbbd8db.crc
diff --git a/...es/GRCh38/MITO/annotations.ht/rows/parts/.part-0-9051c447-510b-49ab-bf6a-cadcf5f69801.crc b/...es/GRCh38/MITO/annotations.ht/rows/parts/.part-0-9051c447-510b-49ab-bf6a-cadcf5f69801.crc
diff --git a/...ixtures/GRCh38/MITO/annotations.ht/rows/parts/part-0-636edbd3-d0a9-410f-b5fe-03749bbbd8db b/...ixtures/GRCh38/MITO/annotations.ht/rows/parts/part-0-636edbd3-d0a9-410f-b5fe-03749bbbd8db
diff --git a/...ixtures/GRCh38/MITO/annotations.ht/rows/parts/part-0-9051c447-510b-49ab-bf6a-cadcf5f69801 b/...ixtures/GRCh38/MITO/annotations.ht/rows/parts/part-0-9051c447-510b-49ab-bf6a-cadcf5f69801
diff --git 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
@@ -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
@@ -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 })