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Fix when exon is resized beyond translationStart #117

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Fix when exon is resized beyond translationStart #117

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49 changes: 49 additions & 0 deletions tests/data/transcripts/input_12.js
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Original file line number Diff line number Diff line change
@@ -0,0 +1,49 @@
define([
'JBrowse/Model/SimpleFeature'
],
function (SimpleFeature) {
// This transcript is corresponding to RefSeq_2
// which is located in file data/RefSeq_2.js
var feature = {
"data": {
"seq_id": "testRefSeq2",
"end": 28,
"start": 1,
"strand": 1,
"subfeatures": [
{
"data": {
"seq_id": "testRefSeq2",
"end": 13,
"start": 1,
"strand": 1,
"type": "exon"
}
},
{
"data": {
"seq_id": "testRefSeq2",
"end": 28,
"start": 18,
"strand": 1,
"type": "exon"
}
},
{
"data": {
"seq_id": "testRefSeq2",
"end": 28,
"start": 18,
"strand": 1,
"type": "CDS"
}
}
],
"type": "transcript"
},
"normalized": true,
};

var transcript = SimpleFeature.fromJSON(feature);
return transcript;
});
49 changes: 49 additions & 0 deletions tests/data/transcripts/resize_5.js
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Original file line number Diff line number Diff line change
@@ -0,0 +1,49 @@
define([
'JBrowse/Model/SimpleFeature'
],
function (SimpleFeature) {
// This transcript is corresponding to RefSeq_2
// which is located in file data/RefSeq_2.js
var feature = {
"data": {
"seq_id": "testRefSeq2",
"end": 28,
"start": 1,
"strand": 1,
"subfeatures": [
{
"data": {
"seq_id": "testRefSeq2",
"end": 13,
"start": 1,
"strand": 1,
"type": "exon"
}
},
{
"data": {
"seq_id": "testRefSeq2",
"end": 28,
"start": 21,
"strand": 1,
"type": "CDS"
}
},
{
"data": {
"seq_id": "testRefSeq2",
"end": 28,
"start": 21,
"strand": 1,
"type": "exon"
}
}
],
"type": "transcript"
},
"normalized": true,
};

var transcript = SimpleFeature.fromJSON(feature);
return transcript;
});
8 changes: 6 additions & 2 deletions tests/data/transcripts/transcript_data.js
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Original file line number Diff line number Diff line change
Expand Up @@ -10,10 +10,12 @@ define([
'./input_9',
'./input_10',
'./input_11',
'./input_12',
'./resize_1',
'./resize_2',
'./resize_3',
'./resize_4',
'./resize_5',
'./orf_1',
'./orf_2',
'./orf_3',
Expand All @@ -36,10 +38,12 @@ define([
input_9,
input_10,
input_11,
input_12,
resize_1,
resize_2,
resize_3,
resize_4,
resize_5,
orf_1,
orf_2,
orf_3,
Expand All @@ -53,8 +57,8 @@ define([
) {
var transcript_data = {
"input": [input_1, input_2, input_3, input_4, input_5, input_6, input_7,
input_8, input_9, input_10, input_11],
"resize": [resize_1, resize_2, resize_3, resize_4],
input_8, input_9, input_10, input_11, input_12],
"resize": [resize_1, resize_2, resize_3, resize_4, resize_5],
"orf": [orf_1, orf_2, orf_3],
"non_canonical": [non_canonical_1, non_canonical_2],
"cds": [cds_1, cds_2],
Expand Down
40 changes: 26 additions & 14 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 @@ -203,25 +203,37 @@ describe( "Edit Track", function() {
expect(compareFeatures(
editTrack.setCDS(transcript_data.input[4], 0, 24),
transcript_data.cds[0])).toBe(true);

var start = editTrack.getTranslationStart(transcript_data.input[1]);
var stop = editTrack.getTranslationStop(transcript_data.input[1]);
var outTranscript = editTrack.setCDS(transcript_data.input[1], start, stop);
expect(compareFeatures(outTranscript, transcript_data.input[1])).toBe(true);
});

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);

exon = editTrack.filterExons(transcript_data.input[11])[1];
right = exon.get('end');
left = exon.get('start') + 3;
outTranscript = editTrack.resizeExon(refSeq, transcript_data.input[11], exon, left, right);
expect(compareFeatures(transcript_data.resize[4], outTranscript)).toBe(true);

// check for the translation start changes
exon = editTrack.filterExons(transcript_data.input[1])[0];
var right = exon.get('end');
var left = exon.get('start') - 3;
right = exon.get('end');
left = exon.get('start') - 3;
outTranscript = editTrack.resizeExon(refSeq, transcript_data.input[1], exon, left, right);
// Verify if CDS is correct
expect(editTrack.getCDS(refSeq, outTranscript)).toEqual(transcript_data.cds[1]);
Expand Down
121 changes: 71 additions & 50 deletions www/JBrowse/View/Track/EditTrack.js
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Original file line number Diff line number Diff line change
Expand Up @@ -645,34 +645,34 @@ var EditTrack = declare(DraggableFeatureTrack,
return;
}

var _exons, exons = [];
var origLeft = exonToResize.get('start');
var origRight = exonToResize.get('end');
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')));
var translationStart = this.getTranslationStart(transcript);
var translationStop = this.getTranslationStop(transcript);

var strand = transcript.get('strand');
if (strand === 1) {
if (left >= translationStart && translationStart >= origLeft) {
translationStart = left;
}
else {
exons.push(this.copyFeature(f));
if (right <= translationStop && translationStop <= origRight) {
translationStop = right;
}
}, 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');
} else {
if (right <= translationStart && translationStart <= origRight) {
translationStart = right;
}
if (translationStart > newTranscript.get('end')) {
translationStart = newTranscript.get('end');
if (left >= translationStop && translationStop >= origLeft) {
translationStop = left;
}
newTranscript = this.setORF(refSeq, newTranscript, translationStart);
}
var newTranscript = this.createTranscript(_exons, transcript.get('name'), refSeq, translationStart, translationStop);
return newTranscript;
},

Expand Down Expand Up @@ -767,17 +767,8 @@ var EditTrack = declare(DraggableFeatureTrack,
var exons = _.reject(this.filterExons(transcript), function (exon) {
return _.indexOf(str_exonsToDelete, JSON.stringify(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 @@ -817,24 +808,8 @@ var EditTrack = declare(DraggableFeatureTrack,
exons = exons.concat(this.filterExons(transcript));
}, this));
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') <= 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));

// 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++);
var name = 'afra-' + exons[0].get('seq_id') + '-mRNA-' + counter++;
var newTranscript = this.createTranscript(exons, name, refSeq, translationStart);
return newTranscript;
},

Expand Down Expand Up @@ -1104,17 +1079,45 @@ var EditTrack = declare(DraggableFeatureTrack,
return transcript;
},

createTranscript: function (subfeatures, name) {
/*
* Create Transcript from the given subfeatures
*
* createTranscripts also combines partially or fully overlapping exons. If
* translation start is not specified then all the non exonic subfeatures
* remain intact. 'setORF' of 'setCDS' is called on the created simplefeature
* depending on if translationStart and translationStop are specified.
*
* If only translationStart is given then 'setORF' is called. And if both
* translationStart and translationStop is 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);

var newexons = [];
_.each(exons, _.bind(function (f) {
var last = newexons[newexons.length - 1];
if (last && (f.get('start') - last.get('end') <= 0)) {
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 {'data': {
Expand All @@ -1134,6 +1137,24 @@ 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);
}
else {
transcript = this.setORF(refSeq, transcript, translationStart);
}
}
return transcript;
},

Expand Down