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Merge pull request #71 from agduncan94/develop
Release 0.1.8
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,114 @@ | ||
| /** | ||
| * Base class for BEDlike files from the GDC | ||
| */ | ||
| define([ | ||
| 'dojo/_base/declare', | ||
| 'dojo/_base/array', | ||
| 'dojo/_base/lang', | ||
| 'JBrowse/Store/SeqFeature/BED', | ||
| './BedLikeParser', | ||
| 'JBrowse/Store/SeqFeature', | ||
| 'JBrowse/Model/XHRBlob', | ||
| 'JBrowse/Model/BlobFilehandleWrapper' | ||
| ], | ||
| function( | ||
| declare, | ||
| array, | ||
| lang, | ||
| BED, | ||
| Parser, | ||
| SeqFeatureStore, | ||
| XHRBlob, | ||
| BlobFilehandleWrapper | ||
| ) { | ||
| return declare([ SeqFeatureStore, BED ], { | ||
| /** | ||
| * Constructor | ||
| * @param {*} args | ||
| */ | ||
| constructor: function (args) { | ||
| this.data = new BlobFilehandleWrapper( | ||
| new XHRBlob( | ||
| this.resolveUrl( | ||
| args.urlTemplate | ||
| ) | ||
| ) | ||
| ); | ||
| }, | ||
|
|
||
| _loadFeatures: function () { | ||
| var thisB = this; | ||
| var features = this.bareFeatures = []; | ||
|
|
||
| var featuresSorted = true; | ||
| var seenRefs = this.refSeqs = {}; | ||
| var parser = new Parser( | ||
| { | ||
| featureCallback: function (fs) { | ||
| array.forEach(fs, function (feature) { | ||
| var prevFeature = features[ features.length - 1 ]; | ||
| var regRefName = thisB.browser.regularizeReferenceName(feature.seq_id); | ||
| if (regRefName in seenRefs && prevFeature && prevFeature.seq_id != feature.seq_id) {featuresSorted = false;} | ||
| if (prevFeature && prevFeature.seq_id == feature.seq_id && feature.start < prevFeature.start) {featuresSorted = false;} | ||
|
|
||
| if (!(regRefName in seenRefs)) {seenRefs[ regRefName ] = features.length;} | ||
|
|
||
| if (thisB.config.featureCallback) { | ||
| features.push(thisB.config.featureCallback(feature, thisB)); | ||
| } else { | ||
| features.push(feature); | ||
| } | ||
| }); | ||
| }, | ||
| endCallback: function () { | ||
| if (!featuresSorted) { | ||
| features.sort(thisB._compareFeatureData); | ||
| // need to rebuild the refseq index if changing the sort order | ||
| thisB._rebuildRefSeqs(features); | ||
| } | ||
|
|
||
| thisB._estimateGlobalStats() | ||
| .then(function (stats) { | ||
| thisB.globalStats = stats; | ||
| thisB._deferred.stats.resolve(); | ||
| }); | ||
|
|
||
| thisB._deferred.features.resolve(features); | ||
| }, | ||
| commentCallback: (this.config.commentCallback || function (i) { }), | ||
| store: this | ||
| }); | ||
|
|
||
| var fail = lang.hitch(this, '_failAllDeferred'); | ||
| // parse the whole file and store it | ||
| let i = 0; | ||
| this.data.fetchLines( | ||
| function (line) { | ||
| try { | ||
| if (i == 0) { | ||
| parser.setExtraFields(line) | ||
| } else { | ||
| // Creates a line where the first columns are BED format and the remaining are extra metadata | ||
| parser.addLine(thisB.convertLineToBED(line)); | ||
| } | ||
| i++; | ||
| } catch (e) { | ||
| fail('Error parsing ' + thisB.getName(), e); | ||
| throw e; | ||
| } | ||
| }, | ||
| lang.hitch(parser, 'finish'), | ||
| fail | ||
| ); | ||
| }, | ||
|
|
||
| /** | ||
| * Stub for getParser | ||
| */ | ||
| getParser: function() { | ||
| return new Promise(function(resolve, reject) { | ||
| resolve({'getMetadata': function() {}}); | ||
| }); | ||
| }, | ||
| }); | ||
| }); |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,59 @@ | ||
| define([ | ||
| 'dojo/_base/declare', | ||
| 'dojo/_base/array', | ||
| 'JBrowse/Store/SeqFeature/BED/Parser', | ||
| ], | ||
| function ( | ||
| declare, | ||
| array, | ||
| Parser | ||
| ) { | ||
| var bed_feature_names = 'seq_id start end name score strand'.split(" "); | ||
| var extra_feature_names = [] | ||
|
|
||
| return declare(Parser, { | ||
| setExtraFields: function(extraFields) { | ||
| extra_feature_names = extraFields.trim().split('\t') | ||
| }, | ||
|
|
||
| parse_feature: function( line ) { | ||
| var f = array.map( line.split("\t"), function(a) { | ||
| if( a == '.' ) { | ||
| return null; | ||
| } | ||
| return a; | ||
| }); | ||
|
|
||
| // unescape only the ref and source columns | ||
| f[0] = this.unescape( f[0] ); | ||
|
|
||
| var parsed = {}; | ||
| const combinedFeatures = bed_feature_names.concat(extra_feature_names) | ||
| for( var i = 0; i < combinedFeatures.length; i++ ) { | ||
| if(f[i]) { | ||
| parsed[ combinedFeatures[i].toLowerCase() ] = f[i] == '.' ? null : f[i]; | ||
| } | ||
| } | ||
|
|
||
| if( parsed.start !== null ) | ||
| parsed.start = parseInt( parsed.start, 10 ); | ||
| if( parsed.end !== null ) | ||
| parsed.end = parseInt( parsed.end, 10 ); | ||
| if( parsed.score != null ) | ||
| parsed.score = parseFloat( parsed.score, 10 ); | ||
|
|
||
| parsed.strand = {'+':1,'-':-1}[parsed.strand] || 0; | ||
|
|
||
| return parsed; | ||
| }, | ||
|
|
||
| unescape(s) { | ||
| if( s === null ) | ||
| return null; | ||
|
|
||
| return s.replace( /%([0-9A-Fa-f]{2})/g, function( match, seq ) { | ||
| return String.fromCharCode( parseInt( seq, 16 ) ); | ||
| }); | ||
| }, | ||
| }); | ||
| }); |
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43 changes: 43 additions & 0 deletions
43
gdc-viewer/js/Store/SeqFeature/IsoformExpressionQuantification.js
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,43 @@ | ||
| /** | ||
| * IsoformExpressionQuantification store class | ||
| * See https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/miRNA_Pipeline/#mirna-expression-workflow | ||
| * | ||
| * Supports (Data format, Data category, Data Type) | ||
| * * TSV, Transcriptome Profiling, Isoform Expression Quantification | ||
| * * TXT, Transcriptome Profiling, Isoform Expression Quantification | ||
| */ | ||
| define([ | ||
| 'dojo/_base/declare', | ||
| './BaseBEDLikeFeature', | ||
| ], | ||
| function ( | ||
| declare, | ||
| BaseBEDLikeFeature | ||
| ) { | ||
| return declare(BaseBEDLikeFeature, { | ||
| // Converts a non-BED file line to BED, and appends the original line to the end | ||
| convertLineToBED: function(line) { | ||
| originalLine = line.split('\t'); | ||
| // Second column contains location in the format refseq:chr:start-end:strand | ||
| // This needs to be redistributed to form BED format | ||
| // Create BED line | ||
| featureLocation = originalLine[1]; | ||
| splitLocation = featureLocation.split(':'); | ||
| splitPos = splitLocation[2].split('-'); | ||
| locationArray = [splitLocation[1].replace('chr', ''), splitPos[0], splitPos[1]]; | ||
|
|
||
| bedLikeLine = locationArray; | ||
| bedLikeLine.push(originalLine[0]) // name | ||
| bedLikeLine.push(originalLine[2]) // score | ||
| bedLikeLine.push(splitLocation[3]) // strand | ||
|
|
||
| // Combine BED line and existing line | ||
| fullLine = bedLikeLine.concat(originalLine) | ||
| return fullLine.join('\t'); | ||
| }, | ||
|
|
||
| getName: function() { | ||
| return 'IsoformExpressionQuantification'; | ||
| }, | ||
| }); | ||
| }); |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,25 @@ | ||
| /** | ||
| * SEG store class for CopyNumberSegment files | ||
| * Supports (Data format, Data category, Data Type) | ||
| * * TXT, Copy number variation, Copy number Segment | ||
| * * TXT, Copy number variation, Masked copy number Segment | ||
| * * TXT, Copy number variation, Allele-specific copy number Segment | ||
| */ | ||
| define([ | ||
| 'dojo/_base/declare', | ||
| './BaseBEDLikeFeature', | ||
| ], | ||
| function ( | ||
| declare, | ||
| BaseBEDLikeFeature | ||
| ) { | ||
| return declare(BaseBEDLikeFeature, { | ||
| convertLineToBED: function(line) { | ||
| return line = line.slice(line.indexOf('\t') + 1); | ||
| }, | ||
|
|
||
| getName: function() { | ||
| return 'SEG' | ||
| } | ||
| }); | ||
| }); |
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