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createTranscript Enhancement
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Signed-off-by: Harsh Gupta <[email protected]>
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@hargup
hargup committed Jan 6, 2015
1 parent ddb595a commit f10390b
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Showing 2 changed files with 71 additions and 63 deletions.
27 changes: 15 additions & 12 deletions tests/js/EditTrack.spec.js
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Original file line number Diff line number Diff line change
Expand Up @@ -103,7 +103,7 @@ describe( "Edit Track", function() {
});

it( 'tests comparison function', function() {
expect(compareFeatures(transcript_data["input"][0], transcript_data["input"][0])).toBe(true);
expect(compareFeatures(transcript_data.input[0], transcript_data.input[0])).toBe(true);
});

it('tests getWholeCDSCoordinates', function() {
Expand Down Expand Up @@ -145,17 +145,20 @@ describe( "Edit Track", function() {
});

it( 'tests resizeExon', function() {
exon = editTrack.filterExons(transcript_data["input"][0])[0];
var right = 17120;
var left = exon.get('start');
outTranscript = editTrack.resizeExon(refSeq, transcript_data["input"][0], exon, left, right);
expect(compareFeatures(transcript_data["resize"][0], outTranscript)).toBe(true);

exon = editTrack.filterExons(transcript_data["input"][1])[1];
var right = exon.get('end') + 3;
var left = exon.get('start');
outTranscript = editTrack.resizeExon(refSeq, transcript_data["input"][1], exon, left, right);
expect(compareFeatures(transcript_data["resize"][2], outTranscript)).toBe(true);
var right, left;

exon = editTrack.filterExons(transcript_data.input[0])[0];
right = 17120;
left = exon.get('start');
outTranscript = editTrack.resizeExon(refSeq, transcript_data.input[0], exon, left, right);
expect(compareFeatures(transcript_data.resize[0], outTranscript)).toBe(true);

exon = editTrack.filterExons(transcript_data.input[1])[1];
right = exon.get('end') + 3;
left = exon.get('start');
outTranscript = editTrack.resizeExon(refSeq, transcript_data.input[1], exon, left, right);
expect(compareFeatures(transcript_data.resize[2], outTranscript)).toBe(true);

});

it( 'tests areOnSameStrand', function() {
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107 changes: 56 additions & 51 deletions www/JBrowse/View/Track/EditTrack.js
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Original file line number Diff line number Diff line change
Expand Up @@ -613,34 +613,15 @@ var EditTrack = declare(DraggableFeatureTrack,
return;
}

var _exons, exons = [];
var _exons;
_exons = this.filterExons(transcript);
_exons = _.reject(_exons, function (exon) { return exon === exonToResize; });
if (left !== right) {
_exons.push(this.copyFeature(exonToResize, {start: left, end: right}));
}
_exons = this.sortAnnotationsByLocation(_exons);
_.each(_exons, _.bind(function (f) {
var last = exons[exons.length - 1];
if (last && (f.get('start') - last.get('end') <= 1)) {
last.set('end', Math.max(last.get('end'), f.get('end')));
}
else {
exons.push(this.copyFeature(f));
}
}, this));

var newTranscript = this.createTranscript(exons, transcript.get('name'));
var translationStart = this.getTranslationStart(transcript);
if (translationStart) {
if (translationStart < newTranscript.get('start')) {
translationStart = newTranscript.get('start');
}
if (translationStart > newTranscript.get('end')) {
translationStart = newTranscript.get('end');
}
newTranscript = this.setORF(refSeq, newTranscript, translationStart);
}
var newTranscript = this.createTranscript(_exons, transcript.get('name'), refSeq, translationStart);
return newTranscript;
},

Expand Down Expand Up @@ -732,17 +713,8 @@ var EditTrack = declare(DraggableFeatureTrack,
var exons = _.reject(this.filterExons(transcript), function (exon) {
return _.indexOf(exonsToDelete, exon) !== -1;
});
var newTranscript = this.createTranscript(exons, transcript.get('name'));
var translationStart = this.getTranslationStart(transcript);
if (translationStart) {
if (translationStart < newTranscript.get('start')) {
translationStart = newTranscript.get('start');
}
if (translationStart > newTranscript.get('end')) {
translationStart = newTranscript.get('end');
}
newTranscript = this.setORF(refSeq, newTranscript, translationStart);
}
var newTranscript = this.createTranscript(exons, transcript.get('name'), translationStart);
return newTranscript;
},

Expand Down Expand Up @@ -782,24 +754,10 @@ var EditTrack = declare(DraggableFeatureTrack,
exons = exons.concat(this.filterExons(transcript));
}, this));
exons = this.sortAnnotationsByLocation(exons);
var name = 'afra-' + exons[0].get('seq_id') + '-mRNA-' + counter++;

// Combine partially or fully overlapping, and immediately adjacent
// exons into one.
var newexons = [];
_.each(exons, _.bind(function (f) {
var last = newexons[newexons.length - 1];
if (last && (f.get('start') - last.get('end') <= 1)) { // we are looking for introns
newexons[newexons.length - 1] = this.copyFeature(last, {end: Math.max(last.get('end'), f.get('end'))});
}
else {
newexons.push(f);
}
}, this));
var newTranscript = this.createTranscript(exons, name, refSeq, translationStart);

// Create new transcript from the processed exons, and insert CDS.
var newTranscript = this.createTranscript(newexons);
newTranscript = this.setORF(refSeq, newTranscript, translationStart);
newTranscript.set('name', 'afra-' + newTranscript.get('seq_id') + '-mRNA-' + counter++);
return newTranscript;
},

Expand Down Expand Up @@ -1069,17 +1027,48 @@ var EditTrack = declare(DraggableFeatureTrack,
return transcript;
},

createTranscript: function (subfeatures, name) {
/**
* Create Transcript from the given subfeatures
*
* createTranscript also combines partially or fully overlapping exons. If
* translation Start is not specified then all the non exonic subfeatures
* remain intact. `setORF` or `setCDS` is called on the created
* simpleFeature depeding on if translationStart and translationStop are
* specified.
* If only translation start is given then setORF is called. And if both
* translationStart and translationStop are given then setCDS is called.
**/
createTranscript: function (subfeatures, name, refSeq, translationStart, translationStop) {
// maintain a count of subfeatures seen, indexed by type
var count = {};

var exons = _.filter(subfeatures, function (f) { return f.get("type") === "exon";});
exons = this.sortAnnotationsByLocation(exons);

// Combine partially or fully overlapping, and immediately adjacent
// exons into one.
var newexons = [];
_.each(exons, _.bind(function (f) {
var last = newexons[newexons.length - 1];
if (last && (f.get('start') - last.get('end') <= 0)) { // we are looking for introns
newexons[newexons.length - 1] = this.copyFeature(last, {end: Math.max(last.get('end'), f.get('end'))});
}
else {
newexons.push(f);
}
}, this));

var nonExons = _.filter(subfeatures, function (f) { return f.get("type") !== "exon";});
var newSubfeatures = nonExons.concat(newexons);
newSubfeatures = this.sortAnnotationsByLocation(newSubfeatures);

var transcript = new SimpleFeature({
data: {
type: 'transcript',
name: name,
seq_id: subfeatures[0].get('seq_id'),
strand: subfeatures[0].get('strand'),
subfeatures: _.map(subfeatures, function (f) {
seq_id: newSubfeatures[0].get('seq_id'),
strand: newSubfeatures[0].get('strand'),
subfeatures: _.map(newSubfeatures, function (f) {
var type = f.get('type');
count[type] = count[type] || 1;
return {
Expand All @@ -1099,6 +1088,22 @@ var EditTrack = declare(DraggableFeatureTrack,
var fmax = _.max(_.map(subfeatures, function (f) { return f.get('end'); }));
transcript.set('start', fmin);
transcript.set('end', fmax);

if (translationStart) {
if (translationStart < fmin) {
translationStart = fmin;
}
if (translationStart > fmax) {
translationStart = fmax;
}
}

if (!_.isUndefined(translationStart) && !_.isUndefined(refSeq)) {
if (!_.isUndefined(translationStop)) {
transcript = this.setCDS(transcript, translationStart, translationStop);
}
transcript = this.setORF(refSeq, transcript, translationStart);
}
return transcript;
},

Expand Down

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