ucsc-xena-client
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UCSC Xena Client. Functional genomics visualizations.
317 lines (227 loc) • 22.3 kB
JavaScript
module.exports =
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/* 0 */
/***/ (function(module, exports, __webpack_require__) {
module.exports = {"allCohorts": __webpack_require__(1),
"allDatasetsN": __webpack_require__(2),
"allFieldMetadata": __webpack_require__(3),
"cohortSamples": __webpack_require__(4),
"cohortSummary": __webpack_require__(5),
"datasetChromProbeValues": __webpack_require__(6),
"datasetFetch": __webpack_require__(7),
"datasetField": __webpack_require__(8),
"datasetFieldExamples": __webpack_require__(9),
"datasetFieldN": __webpack_require__(10),
"datasetGeneProbeAvg": __webpack_require__(11),
"datasetGeneProbesValues": __webpack_require__(12),
"datasetList": __webpack_require__(13),
"datasetMetadata": __webpack_require__(14),
"datasetProbeSignature": __webpack_require__(15),
"datasetProbeValues": __webpack_require__(16),
"datasetSamples": __webpack_require__(17),
"datasetSamplesExamples": __webpack_require__(18),
"datasetSamplesNDenseMatrix": __webpack_require__(19),
"featureList": __webpack_require__(20),
"fieldCodes": __webpack_require__(21),
"fieldMetadata": __webpack_require__(22),
"geneTranscripts": __webpack_require__(23),
"matchFields": __webpack_require__(24),
"maxRange": __webpack_require__(25),
"probemapList": __webpack_require__(26),
"refGeneExons": __webpack_require__(27),
"refGenePosition": __webpack_require__(28),
"refGeneRange": __webpack_require__(29),
"segmentDataExamples": __webpack_require__(30),
"segmentedDataRange": __webpack_require__(31),
"sparseData": __webpack_require__(32),
"sparseDataExamples": __webpack_require__(33),
"sparseDataMatchField": __webpack_require__(34),
"sparseDataMatchFieldSlow": __webpack_require__(35),
"sparseDataMatchPartialField": __webpack_require__(36),
"sparseDataRange": __webpack_require__(37),
"transcriptExpression": __webpack_require__(38)};
/***/ }),
/* 1 */
/***/ (function(module, exports) {
module.exports = ";allCohorts\n(fn []\n\t(map :cohort\n\t (query\n\t\t{:select [[#sql/call [:distinct #sql/call [:ifnull :cohort \"(unassigned)\"]] :cohort]]\n\t\t :from [:dataset]})))\n"
/***/ }),
/* 2 */
/***/ (function(module, exports) {
module.exports = "; allDatasetsN\n(fn []\n\t(count (query {:select [:cohort]\n :from [:dataset]\n :where [:<> :cohort nil]})))\n "
/***/ }),
/* 3 */
/***/ (function(module, exports) {
module.exports = "; allFieldMetadata\n(fn [dataset]\n\t(query {:select [:field.name :feature.*]\n\t\t\t:from [:field]\n\t\t\t:where [:= :dataset_id {:select [:id]\n\t\t\t\t\t\t\t :from [:dataset]\n\t\t\t\t\t\t\t :where [:= :name dataset]}]\n\t\t\t:left-join [:feature [:= :feature.field_id :field.id]]}))\n"
/***/ }),
/* 4 */
/***/ (function(module, exports) {
module.exports = "; cohortSamples\n(fn [cohort limit]\n (map :value\n (query\n {:select [:%distinct.value]\n :from [:dataset]\n :join [:field [:= :dataset.id :dataset_id]\n :code [:= :field_id :field.id]]\n :limit limit\n :where [:and [:= :cohort cohort]\n [:= :field.name \"sampleID\"]]})))\n"
/***/ }),
/* 5 */
/***/ (function(module, exports) {
module.exports = "; cohortSummary\n(fn [exclude]\n\t(query {:select [:cohort [:%count.* :count]]\n\t\t\t:from [:dataset]\n\t\t\t:where [:not [:in :type exclude]]\n\t\t\t:group-by [:cohort]}))\n"
/***/ }),
/* 6 */
/***/ (function(module, exports) {
module.exports = "; datasetChromProbeValues\n(fn [dataset samples chr start end]\n\t(let [probemap (:probemap (car (query {:select [:probemap]\n\t\t\t\t\t\t\t\t\t\t :from [:dataset]\n\t\t\t\t\t\t\t\t\t\t :where [:= :name dataset]})))\n\t\t\tposition (xena-query {:select [\"name\" \"position\"] :from [probemap] :where [:in \"position\" [[chr start end]]]})\n\t\t\tprobes (position \"name\")]\n\t [position\n\t\t(fetch [{:table dataset\n\t\t\t\t :samples samples\n\t\t\t\t :columns probes}])]))\n\n"
/***/ }),
/* 7 */
/***/ (function(module, exports) {
module.exports = "; datasetFetch\n(fn [dataset samples probes]\n (fetch [{:table dataset\n :columns probes\n :samples samples}]))\n"
/***/ }),
/* 8 */
/***/ (function(module, exports) {
module.exports = "; datasetField\n(fn [dataset]\n (map :name (query {:select [:field.name]\n :from [:dataset]\n :join [:field [:= :dataset.id :dataset_id]]\n :where [:= :dataset.name dataset]})))\n"
/***/ }),
/* 9 */
/***/ (function(module, exports) {
module.exports = "; datasetFieldExamples\n(fn [dataset count]\n (map :name (query {:select [:field.name]\n :from [:dataset]\n :join [:field [:= :dataset.id :dataset_id]]\n :where [:= :dataset.name dataset]\n :limit count})))\n"
/***/ }),
/* 10 */
/***/ (function(module, exports) {
module.exports = "; datasetFieldN\n(fn [dataset]\n (:count (car (query {:select [[:%count.field.name :count]]\n :from [:dataset]\n :join [:field [:= :dataset.id :dataset_id]]\n :where [:= :dataset.name dataset]}))))\n"
/***/ }),
/* 11 */
/***/ (function(module, exports) {
module.exports = "; datasetGeneProbeAvg\n(fn [dataset samples genes]\n\t(let [probemap (:probemap (car (query {:select [:probemap]\n\t\t\t\t\t\t\t\t\t\t :from [:dataset]\n\t\t\t\t\t\t\t\t\t\t :where [:= :name dataset]})))\n\t\t get-probes (fn [gene] (xena-query {:select [\"name\" \"position\"] :from [probemap] :where [:in :any \"genes\" [gene]]}))\n\t\t avg (fn [scores] (mean scores 0))\n\t\t scores-for-gene (fn [gene]\n\t\t\t (let [probes (get-probes gene)\n\t\t\t\t\tprobe-names (probes \"name\")\n\t\t\t\t\tscores (fetch [{:table dataset\n\t\t\t\t\t\t\t\t\t:samples samples\n\t\t\t\t\t\t\t\t\t:columns probe-names}])]\n\t\t\t\t{:gene gene\n\t\t\t\t :position (probes \"position\")\n\t\t\t\t :scores (if (car probe-names) (avg scores) [[]])}))]\n\t (map scores-for-gene genes)))\n"
/***/ }),
/* 12 */
/***/ (function(module, exports) {
module.exports = "; datasetGeneProbesValues\n(fn [dataset samples genes]\n\t(let [probemap (:probemap (car (query {:select [:probemap]\n\t\t\t\t\t\t\t\t\t\t :from [:dataset]\n\t\t\t\t\t\t\t\t\t\t :where [:= :name dataset]})))\n\t\t\tposition (xena-query {:select [\"name\" \"position\"] :from [probemap] :where [:in :any \"genes\" genes]})\n\t\t\tprobes (position \"name\")]\n\t [position\n\t\t(fetch [{:table dataset\n\t\t\t\t :samples samples\n\t\t\t\t :columns probes}])]))\n"
/***/ }),
/* 13 */
/***/ (function(module, exports) {
module.exports = "; datasetList\n(fn [cohorts]\n (let [count-table {:select [[:dataset.name :dname] [:%count.value :count]]\n :from [:dataset]\n :join [:field [:= :dataset.id :dataset_id]\n :code [:= :field.id :field_id]]\n :group-by [:dataset.name]\n :where [:= :field.name \"sampleID\"]}]\n (query {:select [:d.name :d.longtitle :count :d.type :d.datasubtype :d.probemap :d.text :d.status [:pm-dataset.text :pmtext]]\n :from [[:dataset :d]]\n :left-join [[:dataset :pm-dataset] [:= :pm-dataset.name :d.probemap]\n count-table [:= :dname :d.name]]\n :where [:in :d.cohort cohorts]})))\n"
/***/ }),
/* 14 */
/***/ (function(module, exports) {
module.exports = "; datasetMetadata\n(fn [dataset]\n (let [count-table {:select [[:dataset.name :dname] [:%count.value :count]]\n :from [:dataset]\n :join [:field [:= :dataset.id :dataset_id]\n :code [:= :field.id :field_id]]\n :group-by [:dataset.name]\n :where [:= :field.name \"sampleID\"]}]\n (query {:select [:d.name :d.longtitle :count :d.type :d.datasubtype :d.probemap :d.text :d.status [:pm-dataset.text :pmtext]]\n :from [[:dataset :d]]\n :left-join [[:dataset :pm-dataset] [:= :pm-dataset.name :d.probemap]\n count-table [:= :dname :d.name]]\n :where [:= :d.name dataset]})))\n"
/***/ }),
/* 15 */
/***/ (function(module, exports) {
module.exports = ";datasetProbeSignature\n(fn [dataset samples probes weights]\n (let [vals (fetch [{:table dataset\n :samples samples\n :columns probes}])]\n (apply + (map (fn [w v] (* v w)) weights vals))))\n"
/***/ }),
/* 16 */
/***/ (function(module, exports) {
module.exports = "; datasetProbeValues\n(fn [dataset samples probes]\n (let [probemap (:probemap (car (query {:select [:probemap]\n :from [:dataset]\n :where [:= :name dataset]})))\n position (if probemap\n ((xena-query {:select [\"name\" \"position\"]\n :from [probemap]\n :where [:in \"name\" probes]}) \"position\")\n nil)]\n [position\n (fetch [{:table dataset\n :columns probes\n :samples samples}])]))\n\n"
/***/ }),
/* 17 */
/***/ (function(module, exports) {
module.exports = "; datasetSamples\n(fn [dataset limit]\n (map :value\n (query\n {:select [:value]\n :from [:dataset]\n :join [:field [:= :dataset.id :dataset_id]\n :code [:= :field.id :field_id]]\n :limit limit\n :where [:and\n [:= :dataset.name dataset]\n [:= :field.name \"sampleID\"]]})))\n"
/***/ }),
/* 18 */
/***/ (function(module, exports) {
module.exports = "; datasetSamplesExamples\n(fn [dataset count]\n\t(map :value\n\t (query\n\t\t{:select [:value]\n\t\t :from [:dataset]\n\t\t :join [:field [:= :dataset.id :dataset_id]\n\t\t\t\t:code [:= :field.id :field_id]]\n\t\t :where [:and\n\t\t\t\t [:= :dataset.name dataset]\n\t\t\t\t [:= :field.name \"sampleID\"]]\n\t\t :limit count})))\n"
/***/ }),
/* 19 */
/***/ (function(module, exports) {
module.exports = "; datasetSamplesNDenseMatrix\n(fn [dataset]\n (map :rows\n (query\n {:select [:rows]\n :from [:dataset]\n :where [:= :name dataset]})))\n"
/***/ }),
/* 20 */
/***/ (function(module, exports) {
module.exports = "; featureList\n(fn [dataset]\n\t(query {:select [:field.name :feature.longtitle]\n\t\t\t:from [:field]\n\t\t\t:where [:= :dataset_id {:select [:id]\n\t\t\t\t\t\t\t :from [:dataset]\n\t\t\t\t\t\t\t :where [:= :name dataset]}]\n\t\t\t:left-join [:feature [:= :feature.field_id :field.id]]}))\n\n"
/***/ }),
/* 21 */
/***/ (function(module, exports) {
module.exports = "; fieldCodes\n(fn [dataset fields]\n\t(query\n\t {:select [:P.name [#sql/call [:group_concat :value :order :ordering :separator #sql/call [:chr 9]] :code]]\n\t :from [[{:select [:field.id :field.name]\n\t\t\t\t:from [:field]\n\t\t\t\t:join [{:table [[[:name :varchar fields]] :T]} [:= :T.name :field.name]]\n\t\t\t\t:where [:= :dataset_id {:select [:id]\n\t\t\t\t\t\t\t\t :from [:dataset]\n\t\t\t\t\t\t\t\t :where [:= :name dataset]}]} :P]]\n\t :left-join [:code [:= :P.id :field_id]]\n\t :group-by [:P.id]}))\n"
/***/ }),
/* 22 */
/***/ (function(module, exports) {
module.exports = "; fieldMetadata\n(fn [dataset fields]\n\t(query\n\t {:select [:P.name :feature.*]\n\t :from [[{:select [:field.name :field.id]\n\t\t\t\t:from [:field]\n\t\t\t\t:join [{:table [[[:name :varchar fields]] :T]} [:= :T.name :field.name]]\n\t\t\t\t:where [:= :dataset_id {:select [:id]\n\t\t\t\t\t\t\t\t :from [:dataset]\n\t\t\t\t\t\t\t\t :where [:= :name dataset]}]} :P]]\n\t :left-join [:feature [:= :feature.field_id :P.id]]}))\n"
/***/ }),
/* 23 */
/***/ (function(module, exports) {
module.exports = "; geneTranscripts\n(fn [dataset gene]\n\t(xena-query {:select [\"name\" \"position (2)\" \"position\" \"exonCount\" \"exonStarts\" \"exonEnds\"]\n\t\t\t\t :from [dataset]\n\t\t\t\t :where [:in :any \"name2\" [gene]]}))\n\n\n"
/***/ }),
/* 24 */
/***/ (function(module, exports) {
module.exports = "; matchFields\n(fn [dataset names]\n\t(map :name (query {:select [:field.name]\n\t\t\t\t\t :from [:dataset]\n\t\t\t\t\t :join [:field [:= :dataset.id :field.dataset_id]]\n\t\t\t\t\t :where [:and [:in :%lower.field.name names] [:= :dataset.name dataset]]})))\n"
/***/ }),
/* 25 */
/***/ (function(module, exports) {
module.exports = "; maxRange\n(fn [dataset chr start end limit]\n\t(let [position (xena-query {:select [\"position\"] :from [dataset]\n :where [:in \"position\" [[chr start end]]]\n :offset limit :limit 1})]\n\t (map :chromstart (position \"position\"))))\n"
/***/ }),
/* 26 */
/***/ (function(module, exports) {
module.exports = ";probemapList\n(fn []\n (query {:select [:name :text]\n :from [:dataset]\n :where [:= :type \"probeMap\"]}))\n"
/***/ }),
/* 27 */
/***/ (function(module, exports) {
module.exports = "; refGeneExons\n(fn [dataset genes]\n (xena-query {:select [\"position (2)\" \"position\" \"exonCount\" \"exonStarts\" \"exonEnds\" \"name2\"]\n :from [dataset]\n :where [:in :any \"name2\" genes]}))\n"
/***/ }),
/* 28 */
/***/ (function(module, exports) {
module.exports = "; refGenePosition\n(fn [dataset gene]\n\t(car ((xena-query {:select [\"position\"] :from [dataset] :where [:in :any \"name2\" [gene]]}) \"position\")))\n"
/***/ }),
/* 29 */
/***/ (function(module, exports) {
module.exports = "; refGeneRange\n(fn [dataset chr start end]\n\t(xena-query {:select [\"position (2)\" \"position\" \"exonCount\" \"exonStarts\" \"exonEnds\" \"name2\"]\n\t\t\t\t:from [dataset]\n\t\t\t\t:where [:in \"position\" [[chr start end]]]}))"
/***/ }),
/* 30 */
/***/ (function(module, exports) {
module.exports = "; sparseDataExample\n(fn [dataset count]\n\t{:rows (xena-query {:select [\"sampleID\" \"position\" \"value\"]\n\t\t\t\t\t\t:from [dataset]\n\t\t\t\t\t\t:limit count})})\n"
/***/ }),
/* 31 */
/***/ (function(module, exports) {
module.exports = "; segmentedDataRange\n(fn [dataset samples chr start end]\n\t(let [getfield (fn [field]\n\t\t\t\t\t (:id (car (query {:select [:field.id]\n\t\t\t\t\t\t\t\t\t :from [:dataset]\n\t\t\t\t\t\t\t\t\t :join [:field [:= :dataset.id :field.dataset_id]]\n\t\t\t\t\t\t\t\t\t :where [:and [:= :field.name field] [:= :dataset.name dataset]]}))))\n\t\t sampleID (getfield \"sampleID\")]\n\t {:samples (map :value (query {:select [:value]\n\t\t\t\t\t\t\t\t\t:from [:code]\n\t\t\t\t\t\t\t\t\t:where [:and [:in :value samples][:= :field_id sampleID]]}))\n\t :rows (xena-query {:select [\"sampleID\" \"position\" \"value\"]\n\t\t\t\t\t\t :from [dataset]\n\t\t\t\t\t\t :where [:and [:in \"position\" [[chr start end]]] [:in \"sampleID\" samples]]})}))\n"
/***/ }),
/* 32 */
/***/ (function(module, exports) {
module.exports = "; sparseData\n(fn [dataset samples genes]\n\t(let [getfield (fn [field]\n\t\t\t\t\t (:id (car (query {:select [:field.id]\n\t\t\t\t\t\t\t\t\t :from [:dataset]\n\t\t\t\t\t\t\t\t\t :join [:field [:= :dataset.id :field.dataset_id]]\n\t\t\t\t\t\t\t\t\t :where [:and [:= :field.name field] [:= :dataset.name dataset]]}))))\n\t\t sampleID (getfield \"sampleID\")]\n\t {:samples (map :value (query {:select [:value]\n\t\t\t\t\t\t\t\t\t:from [:code]\n\t\t\t\t\t\t\t\t\t:where [:and [:in :value samples][:= :field_id sampleID]]}))\n\t :rows (xena-query {:select [\"ref\" \"alt\" \"altGene\" \"effect\" \"dna-vaf\" \"rna-vaf\" \"amino-acid\" \"genes\" \"sampleID\" \"position\"]\n\t\t\t\t\t\t :from [dataset]\n\t\t\t\t\t\t :where [:and [:in :any \"genes\" genes] [:in \"sampleID\" samples]]})}))\n"
/***/ }),
/* 33 */
/***/ (function(module, exports) {
module.exports = "; sparseDataExample\n(fn [dataset count]\n\t{:rows (xena-query {:select [\"ref\" \"alt\" \"altGene\" \"effect\" \"dna-vaf\" \"rna-vaf\" \"amino-acid\" \"genes\" \"sampleID\" \"position\"]\n\t\t\t\t\t\t:from [dataset]\n\t\t\t\t\t\t:limit count})})\n"
/***/ }),
/* 34 */
/***/ (function(module, exports) {
module.exports = "; sparseDataMatchField\n(fn [field dataset names]\n\t(let [getfield (fn [field]\n\t\t\t\t\t (:id (car (query {:select [:field.id]\n\t\t\t\t\t\t\t\t\t :from [:dataset]\n\t\t\t\t\t\t\t\t\t :join [:field [:= :dataset.id :field.dataset_id]]\n\t\t\t\t\t\t\t\t\t :where [:and [:= :field.name field] [:= :dataset.name dataset]]}))))\n\t\t genes (getfield field)]\n\t (map :gene (query {:select [:%distinct.gene]\n\t\t\t\t\t\t :from [:field_gene]\n\t\t\t\t\t\t :join [{:table [[[:name :varchar names]] :T]} [:= :T.name :gene]]\n\t\t\t\t\t\t :where [:= :field_gene.field_id genes]}))))\n"
/***/ }),
/* 35 */
/***/ (function(module, exports) {
module.exports = "; sparseDataMatchFieldSlow\n(fn [field dataset names]\n\t(let [getfield (fn [field]\n\t\t\t\t\t (:id (car (query {:select [:field.id]\n\t\t\t\t\t\t\t\t\t :from [:dataset]\n\t\t\t\t\t\t\t\t\t :join [:field [:= :dataset.id :field.dataset_id]]\n\t\t\t\t\t\t\t\t\t :where [:and [:= :field.name field] [:= :dataset.name dataset]]}))))\n\t\t genes (getfield field)]\n\t (map :gene (query {:select [:%distinct.gene]\n\t\t\t\t\t\t :from [:field_gene]\n\t\t\t\t\t\t :where [:and\n\t\t\t\t\t\t\t\t [:= :field_gene.field_id genes]\n\t\t\t\t\t\t\t\t [:in :%lower.gene names]]}))))\n\n"
/***/ }),
/* 36 */
/***/ (function(module, exports) {
module.exports = "; sparseDataMatchPartialField\n(fn [field dataset names limit]\n\t(let [getfield (fn [field]\n\t\t\t\t\t (:id (car (query {:select [:field.id]\n\t\t\t\t\t\t\t\t\t :from [:dataset]\n\t\t\t\t\t\t\t\t\t :join [:field [:= :dataset.id :field.dataset_id]]\n\t\t\t\t\t\t\t\t\t :where [:and [:= :field.name field] [:= :dataset.name dataset]]}))))\n\t\t genes (getfield field)]\n\t (map :gene (query {:select [:%distinct.gene]\n\t\t\t\t\t\t :limit limit\n\t\t\t\t\t\t :order-by [:gene]\n\t\t\t\t\t\t :from [:field_gene]\n\t\t\t\t\t\t :join [{:table [[[:name :varchar names]] :T]} [:like :gene :T.name]]\n\t\t\t\t\t\t :where [:= :field_gene.field_id genes]}))))\n"
/***/ }),
/* 37 */
/***/ (function(module, exports) {
module.exports = "; sparseDataRange\n(fn [dataset samples chr start end]\n\t(let [getfield (fn [field]\n\t\t\t\t\t (:id (car (query {:select [:field.id]\n\t\t\t\t\t\t\t\t\t :from [:dataset]\n\t\t\t\t\t\t\t\t\t :join [:field [:= :dataset.id :field.dataset_id]]\n\t\t\t\t\t\t\t\t\t :where [:and [:= :field.name field] [:= :dataset.name dataset]]}))))\n\t\t sampleID (getfield \"sampleID\")]\n\t {:samples (map :value (query {:select [:value]\n\t\t\t\t\t\t\t\t\t:from [:code]\n\t\t\t\t\t\t\t\t\t:where [:and [:in :value samples][:= :field_id sampleID]]}))\n\t :rows (xena-query {:select [\"ref\" \"alt\" \"altGene\" \"effect\" \"dna-vaf\" \"rna-vaf\" \"amino-acid\" \"genes\" \"sampleID\" \"position\"]\n\t\t\t\t\t\t :from [dataset]\n\t\t\t\t\t\t :where [:and [:in \"position\" [[chr start end]]] [:in \"sampleID\" samples]]})}))\n"
/***/ }),
/* 38 */
/***/ (function(module, exports) {
module.exports = "; transcriptExpression\n(fn [transcripts studyA subtypeA studyB subtypeB dataset]\n (let [tcgaTypes\n (map :value (query {:select [:value]\n :from [:code]\n :join [:field [:= :field_id :field.id]\n :dataset [:= :dataset_id :dataset.id]]\n :where [:and [:= :dataset.name \"TcgaTargetGTEX_phenotype.txt\"]\n [:= :field.name \"_sample_type\"]\n [:not= :value [\"Control Analyte\" \"Solid Tissue Normal\"]]]}))\n fetchSamples {\n \"tcga\" (fn [subtype]\n ((xena-query {:select [\"sampleID\"]\n :from [\"TcgaTargetGTEX_phenotype.txt\"]\n :where [:and [:in \"_study\" [\"TCGA\"]]\n [:in \"_sample_type\" tcgaTypes]\n [:in \"detailed_category\" [subtype]]]}) \"sampleID\"))\n \"gtex\" (fn [subtype]\n ((xena-query {:select [\"sampleID\"]\n :from [\"TcgaTargetGTEX_phenotype.txt\"]\n :where [:and [:in \"_study\" [\"GTEX\"]]\n [:in \"_sample_type\" [\"Normal Tissue\"]]\n [:in \"_primary_site\" [subtype]]]}) \"sampleID\"))}]\n [(fetch [{:table dataset\n :columns transcripts\n :samples ((fetchSamples studyA) subtypeA)}])\n (fetch [{:table dataset\n :columns transcripts\n :samples ((fetchSamples studyB) subtypeB)}])]))\n"
/***/ })
/******/ ]);