From b1da60b4ff6acdc421dadbfdf336684c88d73e33 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 14 Oct 2024 16:28:39 -0400 Subject: [PATCH 1/2] mito local constraint --- .../GRCh38/MITO/annotations.ht/.README.txt.crc | Bin 12 -> 0 bytes .../GRCh38/MITO/annotations.ht/._SUCCESS.crc | Bin 8 -> 0 bytes .../MITO/annotations.ht/.metadata.json.gz.crc | Bin 16 -> 0 bytes .../GRCh38/MITO/annotations.ht/README.txt | 3 --- .../fixtures/GRCh38/MITO/annotations.ht/_SUCCESS | 0 .../annotations.ht/globals/.metadata.json.gz.crc | Bin 16 -> 0 bytes .../MITO/annotations.ht/globals/metadata.json.gz | Bin 619 -> 0 bytes .../annotations.ht/globals/parts/.part-0.crc | Bin 24 -> 0 bytes .../MITO/annotations.ht/globals/parts/part-0 | Bin 1692 -> 0 bytes .../.index.crc | Bin 12 -> 0 bytes .../.metadata.json.gz.crc | Bin 12 -> 0 bytes .../index | Bin 95 -> 0 bytes .../metadata.json.gz | Bin 185 -> 0 bytes .../GRCh38/MITO/annotations.ht/metadata.json.gz | Bin 829 -> 0 bytes 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hail_search/fixtures/GRCh38/MITO/annotations.ht/rows/metadata.json.gz delete mode 100644 hail_search/fixtures/GRCh38/MITO/annotations.ht/rows/parts/.part-0-9051c447-510b-49ab-bf6a-cadcf5f69801.crc delete mode 100644 hail_search/fixtures/GRCh38/MITO/annotations.ht/rows/parts/part-0-9051c447-510b-49ab-bf6a-cadcf5f69801 diff --git a/hail_search/fixtures/GRCh38/MITO/annotations.ht/.README.txt.crc b/hail_search/fixtures/GRCh38/MITO/annotations.ht/.README.txt.crc deleted file mode 100644 index 4937f949dee5571c61980258b96e966a6688b992..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 12 TcmYc;N@ieSU}AV8Z&wNc5?%uF diff --git a/hail_search/fixtures/GRCh38/MITO/annotations.ht/._SUCCESS.crc b/hail_search/fixtures/GRCh38/MITO/annotations.ht/._SUCCESS.crc deleted file mode 100644 index 3b7b044936a890cd8d651d349a752d819d71d22c..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 8 PcmYc;N@ieSU}69O2$TUk 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 deleted file mode 100644 index 679f60ca2c66a8cb81a7993458f6c326d9d1b645..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 16 XcmYc;N@ieSU}7lK=-=;jIaeG2BD(~@ diff --git a/hail_search/fixtures/GRCh38/MITO/annotations.ht/README.txt b/hail_search/fixtures/GRCh38/MITO/annotations.ht/README.txt deleted file mode 100644 index c1f060502b..0000000000 --- a/hail_search/fixtures/GRCh38/MITO/annotations.ht/README.txt +++ /dev/null @@ -1,3 +0,0 @@ -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 diff --git a/hail_search/fixtures/GRCh38/MITO/annotations.ht/_SUCCESS b/hail_search/fixtures/GRCh38/MITO/annotations.ht/_SUCCESS deleted file mode 100644 index e69de29bb2..0000000000 diff --git 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PredictionPath('local_constraint_mito', 'score'), } PATHOGENICITY_FILTERS = { diff --git a/hail_search/test_utils.py b/hail_search/test_utils.py index 267fc9acb1..7221549a04 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 3415a1287e..d950a6b30e 100644 --- a/ui/shared/utils/constants.js +++ b/ui/shared/utils/constants.js @@ -1454,6 +1454,7 @@ 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('#') ? 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