From 6b45c21e99b9958b9b4c093f6c25bb3f7dc0ee2e Mon Sep 17 00:00:00 2001 From: Colin Date: Thu, 14 Mar 2024 18:07:36 -0400 Subject: [PATCH] Clear selection --- package.json | 1 + src/mappings.ts | 44 +------ yarn.lock | 331 +++++++++++++++++++++++++++++++----------------- 3 files changed, 216 insertions(+), 160 deletions(-) diff --git a/package.json b/package.json index 44e822e..abdbf27 100644 --- a/package.json +++ b/package.json @@ -23,6 +23,7 @@ "dependencies": { "@mui/icons-material": "^5.15.10", "clustal-js": "^2.0.1", + "g2p_mapper": "^1.0.3", "molstar": "^4.0.0", "pako": "^2.1.0" }, diff --git a/src/mappings.ts b/src/mappings.ts index 4c3bd70..24ac624 100644 --- a/src/mappings.ts +++ b/src/mappings.ts @@ -1,4 +1,5 @@ import { Feature } from '@jbrowse/core/util' +import { genomeToTranscriptSeqMapping as g2p } from 'g2p_mapper' export interface Alignment { alns: { @@ -83,45 +84,6 @@ export function transcriptPositionToAlignmentMap(alignment: Alignment) { // see similar function in msaview plugin export function genomeToTranscriptSeqMapping(feature: Feature) { - const strand = feature.get('strand') as number - const refName = feature.get('refName') - const subs = feature.children() ?? [] - const cds = subs - .filter(f => f.get('type') === 'CDS') - .sort((a, b) => strand * (a.get('start') - b.get('start'))) - const g2p = {} as Record - const p2g = {} as Record - - let proteinCounter = 0 - if (strand !== -1) { - for (const f of cds) { - for ( - let genomePos = f.get('start'); - genomePos < f.get('end'); - genomePos++ - ) { - const proteinPos = Math.floor(proteinCounter++ / 3) - g2p[genomePos] = proteinPos - if (!p2g[proteinPos]) { - p2g[proteinPos] = genomePos - } - } - } - } else { - for (const f of cds) { - for ( - let genomePos = f.get('end'); - genomePos > f.get('start'); - genomePos-- - ) { - const proteinPos = Math.floor(proteinCounter++ / 3) - g2p[genomePos] = proteinPos - if (!p2g[proteinPos]) { - p2g[proteinPos] = genomePos - } - } - } - } - - return { g2p, p2g, refName, strand } + // @ts-expect-error + return g2p(feature.toJSON()) } diff --git a/yarn.lock b/yarn.lock index 33145d5..d1caff3 100644 --- a/yarn.lock +++ b/yarn.lock @@ -1267,9 +1267,9 @@ form-data "^4.0.0" "@types/node@*", "@types/node@^20.11.16": - 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version "7.34.0" - resolved "https://registry.yarnpkg.com/eslint-plugin-react/-/eslint-plugin-react-7.34.0.tgz#ab71484d54fc409c37025c5eca00eb4177a5e88c" - integrity sha512-MeVXdReleBTdkz/bvcQMSnCXGi+c9kvy51IpinjnJgutl3YTHWsDdke7Z1ufZpGfDG8xduBDKyjtB9JH1eBKIQ== + version "7.34.1" + resolved "https://registry.yarnpkg.com/eslint-plugin-react/-/eslint-plugin-react-7.34.1.tgz#6806b70c97796f5bbfb235a5d3379ece5f4da997" + integrity sha512-N97CxlouPT1AHt8Jn0mhhN2RrADlUAsk1/atcT2KyA/l9Q/E6ll7OIGwNumFmWfZ9skV3XXccYS19h80rHtgkw== dependencies: array-includes "^3.1.7" array.prototype.findlast "^1.2.4" @@ -2942,6 +3020,13 @@ functions-have-names@^1.2.3: resolved "https://registry.yarnpkg.com/functions-have-names/-/functions-have-names-1.2.3.tgz#0404fe4ee2ba2f607f0e0ec3c80bae994133b834" integrity sha512-xckBUXyTIqT97tq2x2AMb+g163b5JFysYk0x4qxNFwbfQkmNZoiRHb6sPzI9/QV33WeuvVYBUIiD4NzNIyqaRQ== +g2p_mapper@^1.0.3: + version "1.0.4" + resolved "https://registry.yarnpkg.com/g2p_mapper/-/g2p_mapper-1.0.4.tgz#243730c33d92b093f61a18b05479465f67bd8612" + integrity sha512-Os3yuQZcTSuGbO4A7NuXmcfIu80IeOjyZYZ4Eow9Af0sb6IlcmymcA99gYjRUk4enKjRFAXjnCw6Y4rw7S7yww== + dependencies: + yargs "^17.7.2" + generic-filehandle@^3.0.0: version "3.1.2" resolved "https://registry.yarnpkg.com/generic-filehandle/-/generic-filehandle-3.1.2.tgz#3b5f4cc927f7833d2d90157e0b12ce235526fa41" @@ -3118,7 +3203,7 @@ has-tostringtag@^1.0.0, has-tostringtag@^1.0.2: dependencies: has-symbols "^1.0.3" -hasown@^2.0.0, hasown@^2.0.1: +hasown@^2.0.0, hasown@^2.0.1, hasown@^2.0.2: version "2.0.2" resolved "https://registry.yarnpkg.com/hasown/-/hasown-2.0.2.tgz#003eaf91be7adc372e84ec59dc37252cedb80003" integrity sha512-0hJU9SCPvmMzIBdZFqNPXWa6dqh7WdH0cII9y+CyS8rG3nL48Bclra9HmKhVVUHyPWNH5Y7xDwAB7bfgSjkUMQ== @@ -3344,6 +3429,13 @@ is-core-module@^2.13.0: dependencies: hasown "^2.0.0" +is-data-view@^1.0.1: + version "1.0.1" + resolved "https://registry.yarnpkg.com/is-data-view/-/is-data-view-1.0.1.tgz#4b4d3a511b70f3dc26d42c03ca9ca515d847759f" + integrity sha512-AHkaJrsUVW6wq6JS8y3JnM/GJF/9cf+k20+iDzlSaJrinEo5+7vRiteOSwBhHRiAyQATN1AmY4hwzxJKPmYf+w== + dependencies: + is-typed-array "^1.1.13" + is-date-object@^1.0.1, is-date-object@^1.0.5: version "1.0.5" resolved "https://registry.yarnpkg.com/is-date-object/-/is-date-object-1.0.5.tgz#0841d5536e724c25597bf6ea62e1bd38298df31f" @@ -4752,13 +4844,13 @@ object.hasown@^1.1.3: es-abstract "^1.22.1" object.values@^1.1.6, object.values@^1.1.7: - 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call-bind "^1.0.5" + call-bind "^1.0.7" define-properties "^1.2.1" - es-abstract "^1.22.3" - es-errors "^1.0.0" - get-intrinsic "^1.2.3" + es-abstract "^1.23.1" + es-errors "^1.3.0" + get-intrinsic "^1.2.4" globalthis "^1.0.3" which-builtin-type "^1.1.3" @@ -5322,7 +5414,7 @@ rxjs@^7.0.0, rxjs@^7.8.1: dependencies: tslib "^2.1.0" -safe-array-concat@^1.0.0, safe-array-concat@^1.1.0: +safe-array-concat@^1.0.0, safe-array-concat@^1.1.0, safe-array-concat@^1.1.2: version "1.1.2" resolved "https://registry.yarnpkg.com/safe-array-concat/-/safe-array-concat-1.1.2.tgz#81d77ee0c4e8b863635227c721278dd524c20edb" integrity sha512-vj6RsCsWBCf19jIeHEfkRMw8DPiBb+DMXklQ/1SGDHOMlHdPUkZXFQ2YdplS23zESTijAcurb1aSgJA3AgMu1Q== @@ -5503,9 +5595,9 @@ slash@^3.0.0: integrity sha512-g9Q1haeby36OSStwb4ntCGGGaKsaVSjQ68fBxoQcutl5fS1vuY18H3wSt3jFyFtrkx+Kz0V1G85A4MyAdDMi2Q== source-map-js@^1.0.2: - version "1.0.2" - resolved "https://registry.yarnpkg.com/source-map-js/-/source-map-js-1.0.2.tgz#adbc361d9c62df380125e7f161f71c826f1e490c" - integrity sha512-R0XvVJ9WusLiqTCEiGCmICCMplcCkIwwR11mOSD9CR5u+IXYdiseeEuXCVAjS54zqwkLcPNnmU4OeJ6tUrWhDw== + version "1.1.0" + resolved "https://registry.yarnpkg.com/source-map-js/-/source-map-js-1.1.0.tgz#9e7d5cb46f0689fb6691b30f226937558d0fa94b" + integrity sha512-9vC2SfsJzlej6MAaMPLu8HiBSHGdRAJ9hVFYN1ibZoNkeanmDmLUcIrj6G9DGL7XMJ54AKg/G75akXl1/izTOw== source-map-support@0.5.13: version "0.5.13" @@ -5627,23 +5719,24 @@ string.prototype.padend@^3.0.0: define-properties "^1.2.0" es-abstract "^1.22.1" -string.prototype.trim@^1.2.8: - version "1.2.8" - resolved "https://registry.yarnpkg.com/string.prototype.trim/-/string.prototype.trim-1.2.8.tgz#f9ac6f8af4bd55ddfa8895e6aea92a96395393bd" - integrity sha512-lfjY4HcixfQXOfaqCvcBuOIapyaroTXhbkfJN3gcB1OtyupngWK4sEET9Knd0cXd28kTUqu/kHoV4HKSJdnjiQ== +string.prototype.trim@^1.2.8, string.prototype.trim@^1.2.9: + version "1.2.9" + resolved "https://registry.yarnpkg.com/string.prototype.trim/-/string.prototype.trim-1.2.9.tgz#b6fa326d72d2c78b6df02f7759c73f8f6274faa4" + integrity sha512-klHuCNxiMZ8MlsOihJhJEBJAiMVqU3Z2nEXWfWnIqjN0gEFS9J9+IxKozWWtQGcgoa1WUZzLjKPTr4ZHNFTFxw== dependencies: - call-bind "^1.0.2" - define-properties "^1.2.0" - es-abstract "^1.22.1" + call-bind "^1.0.7" + define-properties "^1.2.1" + es-abstract "^1.23.0" + es-object-atoms "^1.0.0" -string.prototype.trimend@^1.0.7: - version "1.0.7" - resolved "https://registry.yarnpkg.com/string.prototype.trimend/-/string.prototype.trimend-1.0.7.tgz#1bb3afc5008661d73e2dc015cd4853732d6c471e" - integrity sha512-Ni79DqeB72ZFq1uH/L6zJ+DKZTkOtPIHovb3YZHQViE+HDouuU4mBrLOLDn5Dde3RF8qw5qVETEjhu9locMLvA== +string.prototype.trimend@^1.0.7, string.prototype.trimend@^1.0.8: + version "1.0.8" + resolved "https://registry.yarnpkg.com/string.prototype.trimend/-/string.prototype.trimend-1.0.8.tgz#3651b8513719e8a9f48de7f2f77640b26652b229" + integrity sha512-p73uL5VCHCO2BZZ6krwwQE3kCzM7NKmis8S//xEC6fQonchbum4eP6kR4DLEjQFO3Wnj3Fuo8NM0kOSjVdHjZQ== dependencies: - call-bind "^1.0.2" - define-properties "^1.2.0" - es-abstract "^1.22.1" + call-bind "^1.0.7" + define-properties "^1.2.1" + es-object-atoms "^1.0.0" string.prototype.trimstart@^1.0.7: version "1.0.7" @@ -6188,7 +6281,7 @@ which-collection@^1.0.1: is-weakmap "^2.0.2" is-weakset "^2.0.3" -which-typed-array@^1.1.14, which-typed-array@^1.1.9: +which-typed-array@^1.1.14, which-typed-array@^1.1.15, which-typed-array@^1.1.9: version "1.1.15" resolved "https://registry.yarnpkg.com/which-typed-array/-/which-typed-array-1.1.15.tgz#264859e9b11a649b388bfaaf4f767df1f779b38d" integrity sha512-oV0jmFtUky6CXfkqehVvBP/LSWJ2sy4vWMioiENyJLePrBO/yKyV9OyJySfAKosh+RYkIl5zJCNZ8/4JncrpdA== @@ -6278,7 +6371,7 @@ yargs-parser@^21.0.1, yargs-parser@^21.1.1: resolved "https://registry.yarnpkg.com/yargs-parser/-/yargs-parser-21.1.1.tgz#9096bceebf990d21bb31fa9516e0ede294a77d35" integrity sha512-tVpsJW7DdjecAiFpbIB1e3qxIQsE6NoPc5/eTdrbbIC4h0LVsWhnoa3g+m2HclBIujHzsxZ4VJVA+GUuc2/LBw== -yargs@^17.3.1: +yargs@^17.3.1, yargs@^17.7.2: version "17.7.2" resolved "https://registry.yarnpkg.com/yargs/-/yargs-17.7.2.tgz#991df39aca675a192b816e1e0363f9d75d2aa269" integrity sha512-7dSzzRQ++CKnNI/krKnYRV7JKKPUXMEh61soaHKg9mrWEhzFWhFnxPxGl+69cD1Ou63C13NUPCnmIcrvqCuM6w==