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Simplification of features #21

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641e866
deal with start/end for features of type "Other". Avoid the creation …
FredericBGA Dec 2, 2020
64d1ee5
better names for function and variable
FredericBGA Dec 3, 2020
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155 changes: 95 additions & 60 deletions js/main.js
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Original file line number Diff line number Diff line change
Expand Up @@ -68,6 +68,7 @@ return declare( JBrowsePlugin,

},


/**
* Title: _prepareAndLaunch
* Description: Creates deferred feature and sequence objects
Expand All @@ -94,7 +95,7 @@ return declare( JBrowsePlugin,

var feat = results[0][1];
var seq = results[1][1];
var opt = {};
var opt = {};
//var opt = {seqDivName: 'seq_display'};

//To export the FeatureSequence object in JSON, uncomment the following:
Expand Down Expand Up @@ -169,10 +170,8 @@ return declare( JBrowsePlugin,
var myName = '';
for (var cachedStore in cache) {
var attr = cache[cachedStore].store;
//console.log(attr.name);
if (attr.hasOwnProperty('fasta') && attr.hasOwnProperty('name')){
myName = attr.name;
//console.log(attr.name+" is your indexed_fasta store!");
}else if (attr.hasOwnProperty('name') && attr.name === 'refseqs') {
myName = attr.name;
}
Expand All @@ -191,9 +190,9 @@ return declare( JBrowsePlugin,
}
my_browser.getStore('refseqs', dojo.hitch(this,function( refSeqStore ) {

if( refSeqStore ) {
refSeqStore.getReferenceSequence(
{ ref: my_browser.refSeq.name, start: getStart, end: getEnd},
if( refSeqStore ) {
refSeqStore.getReferenceSequence(
{ ref: my_browser.refSeq.name, start: getStart, end: getEnd},
dojo.hitch( this, function (fullSeq){
if (feature.get('strand') == -1) {
fullSeq = Util.revcom(fullSeq);
Expand Down Expand Up @@ -245,6 +244,31 @@ return declare( JBrowsePlugin,
},


/**
* Title: _canAddFeat
* Description: Checks if there's a feature that shares the same boundaries
* in the list of features.
* It checks the start and end positions and if the feature type holds
* the optionnal string.
* @param {features (an array of feature objects), feature (a single feature object), type (a string, the type of feature)}
* @returns {0|1 (1 if feature is not in features and can be added, 0 otherwise)}
*/
_canAddFeat: function(features, feature, type = null) {
for (const single_feat of features) {
if (type) {
if (single_feat.start == feature.start && single_feat.end == feature.end && feature.type.includes(type)) {
return 0;
}
} else {
if (single_feat.start == feature.start && single_feat.end == feature.end) {
return 0;
}
}
}
return 1;
},


/**
* Title: _getSubFeats
* Description: Creates a sorted array of subfeatures,
Expand All @@ -255,33 +279,33 @@ return declare( JBrowsePlugin,
_getSubFeats: function (feature) {
//console.log("Calling getSubFeats"); //TWS DEBUG

var feature_coords = [feature.get('start'), feature.get('end')]
var feature_coords = [feature.get('start'), feature.get('end')]
.sort(function(a,b){return a-b;}); //swap if out of order

var feature_strand = feature.get('strand');
var feature_strand = feature.get('strand');

var types = [];
//var subfeatures = [{'start':subf_start, 'end':subf_end, 'strand':subf_strand, 'type':subf_type, 'id': subf_type+'_'+(ind+1)}];
var subfeatures = [];

feature.get('subfeatures').forEach(function(f, ind) {
feature.get('subfeatures').forEach(function(f, ind) {

var subfeat_coords = [f.get('start'), f.get('end')]
var subfeat_coords = [f.get('start'), f.get('end')]
.sort(function(a,b){return a-b;}); //swap if out of order

//All coordinates are made relative to feature start
if (feature_strand == 1) {
var subf_start = subfeat_coords[0] - feature_coords[0];
var subf_end = subfeat_coords[1] - feature_coords[0];
} else if (feature_strand == -1) {
var subf_start = feature_coords[1] - subfeat_coords[1];
var subf_end = feature_coords[1] - subfeat_coords[0];
}
if (feature_strand == 1) {
var subf_start = subfeat_coords[0] - feature_coords[0];
var subf_end = subfeat_coords[1] - feature_coords[0];
} else if (feature_strand == -1) {
var subf_start = feature_coords[1] - subfeat_coords[1];
var subf_end = feature_coords[1] - subfeat_coords[0];
}

var subf_strand = f.get('strand');
var subf_type = f.get('type');
var subf_strand = f.get('strand');
var subf_type = f.get('type');

var subf_obj = {'start':subf_start, 'end':subf_end, 'strand':subf_strand, 'type':subf_type, 'id': subf_type+'_'+(ind+1)};
var subf_obj = {'start':subf_start, 'end':subf_end, 'strand':subf_strand, 'type':subf_type, 'id': subf_type+'_'+(ind+1)};

//Push subf_type to types array if not seen yet
if (array.indexOf(types, subf_type) === -1 ) {
Expand All @@ -290,12 +314,11 @@ return declare( JBrowsePlugin,

subfeatures.push(subf_obj)

});
});

var overlaps = this._checkForOverlap(subfeatures.sort(function(a,b){return a.start - b.start}));
var overlaps = this._checkForOverlap(subfeatures.sort(function(a,b){return a.start - b.start}));
if (overlaps === -1) {
// If no overlap, fill in the blanks
//fillscan(rel_coords, subfeatures)
subfeatures = this._fillScan({
start: 0,
end: Math.abs(feature.get('end') - feature.get('start'))
Expand All @@ -308,11 +331,10 @@ return declare( JBrowsePlugin,
start: 0,
end: Math.abs(feature.get('end') - feature.get('start'))
}, cleanedSubfeats.sort(function(a,b){return a.start - b.start}));
//console.log(overlaps);
}
}

//console.log(subfeatures); //TWS DEBUG
return subfeatures;
return subfeatures;
},

/**
Expand All @@ -323,18 +345,18 @@ return declare( JBrowsePlugin,
*/
intronsFromExons: function (exons) {

//console.log("Calling intronsFromExons"); //TWS DEBUG
var intronArray = [];
//console.log("Calling intronsFromExons"); //TWS DEBUG
var intronArray = [];

for (var i = 0; i < exons.length-1; i++) {
for (var i = 0; i < exons.length-1; i++) {

var intron_start = exons[i].end;
var intron_end = exons[i+1].start;
var intron_start = exons[i].end;
var intron_end = exons[i+1].start;

intronArray[i] = {'start':intron_start,'end':intron_end, 'strand':exons[i].strand, 'type':'intron', 'id': 'intron_'+(i+1)};
intronArray[i] = {'start':intron_start,'end':intron_end, 'strand':exons[i].strand, 'type':'intron', 'id': 'intron_'+(i+1)};
}
return intronArray;
return intronArray;
},

/**
Expand All @@ -345,7 +367,7 @@ return declare( JBrowsePlugin,
*/
sortByKey: function (array, key) {

//console.log("Calling sortByKey"); //TWS DEBUG
//console.log("Calling sortByKey"); //TWS DEBUG
return array.sort(function(a, b) {
var x = a[key];
var y = b[key];
Expand Down Expand Up @@ -378,6 +400,7 @@ return declare( JBrowsePlugin,
return types;
},


/**
* Title: fillScan
* Description: Scan through array of subfeatures and fill in spaces
Expand All @@ -390,17 +413,21 @@ return declare( JBrowsePlugin,
_fillScan: function (coords, subfeatures) {
//console.log("Calling fillScan"); //TWS DEBUG

var gaps = [];
var gaps = [];
//Give the non-annotated regions a default type name
var defaultType = 'other';

if (subfeatures[0].start != coords.start) {
//console.log("Filling in the start");
var feat = {start: coords.start, end: subfeatures[0].start, type: defaultType, id: defaultType+'_a'}
gaps.push(feat);
if (subfeatures[0].start != coords.start) {
// console.log("Filling in the start");
if (coords.start < subfeatures[0].start) {
var feat = {start: coords.start, end: subfeatures[0].start, type: defaultType, id: defaultType+'_a'}
} else {
var feat = {start: subfeatures[0].start, end: coords.start, type: defaultType, id: defaultType+'_a'}
}
this._canAddFeat(subfeatures, feat) && gaps.push(feat);
}

//console.log("Filling in the middle bits");
// console.log("Filling in the middle bits");
for (i = 0; i < subfeatures.length - 1; i++) {

//If current and next subfeature are the same and are 'exon' or 'CDS', type is intron
Expand All @@ -413,26 +440,30 @@ return declare( JBrowsePlugin,
}

//Do the actual filling in: create feature and push to array
if ( subfeatures[i].end != subfeatures[i+1].start) {
var feat = {start: subfeatures[i].end, end: subfeatures[i+1].start, type: newType , id: newType+i };
gaps.push(feat);
if ( subfeatures[i].end != subfeatures[i+1].start) {
if (subfeatures[i].end < subfeatures[i+1].start) {
var feat = {start: subfeatures[i].end, end: subfeatures[i+1].start, type: newType , id: newType+i };
} else {
var feat = {start: subfeatures[i+1].start, end: subfeatures[i].end, type: newType , id: newType+i };
}
this._canAddFeat(subfeatures, feat) && gaps.push(feat);
}
}

if (subfeatures[subfeatures.length - 1].end != coords.end) {
//console.log("Filling in the end");
var feat = {start: subfeatures[subfeatures.length - 1].end, end: coords.end, type: defaultType, id: defaultType+'_z' };
// console.log("Filling in the end");
if (subfeatures[subfeatures.length - 1].end < coords.end) {
var feat = {start: subfeatures[subfeatures.length - 1].end, end: coords.end, type: defaultType, id: defaultType+'_z' };
} else {
var feat = {start: coords.end, start: subfeatures[subfeatures.length - 1].end, type: defaultType, id: defaultType+'_z' };
}
gaps.push(feat);
}

//return gaps;

//Add gaps to subfeatures and re-sort by start, then return result
return subfeatures.concat(gaps).sort(function(a,b){return a.start - b.start});


//return subfeatures;

},

_checkForOverlap: function(subfeatures) {
Expand All @@ -456,7 +487,7 @@ return declare( JBrowsePlugin,
* @param {overlaps(Array), allFeatures(Array)}
* @returns {allFeatures(Array)}
*/
_cleanOverlaps: function(overlaps, allFeatures) {
_cleanOverlaps: function(overlaps, allFeatures) {
overlaps.forEach(function(pair, ind) {
//Make sure both objects in pair are of type 'CDS' and 'exon'
var goodTypes = pair.filter(function(obj) {
Expand Down Expand Up @@ -484,6 +515,8 @@ return declare( JBrowsePlugin,
.indexOf(mod_name); //find
allFeatures[modStart_indx].start = new_exonStart; //modify
allFeatures[modStart_indx].type = "UTR"; //modify
var canAdd = this._canAddFeat(allFeatures, allFeatures[modStart_indx], 'UTR');
(!canAdd) && allFeatures.splice(modStart_indx, 1); //remove
} else if (pair[0].end == pair[1].end) {
//Ends match but starts dont. Modify exon end to not overlap, change to UTR
var new_exonEnd = pair[CDSObjIndx].start;
Expand All @@ -492,6 +525,8 @@ return declare( JBrowsePlugin,
.indexOf(mod_name); // find
allFeatures[modEnd_indx].end = new_exonEnd; //modify
allFeatures[modEnd_indx].type = "UTR"; //modify
var canAdd = this._canAddFeat(allFeatures, allFeatures[modEnd_indx], 'UTR');
(!canAdd) && allFeatures.splice(modEnd_indx, 1); //remove
} else {
// One completely within another. Replace exon with 5'UTR and
// also add in a 3'UTR
Expand All @@ -512,9 +547,9 @@ return declare( JBrowsePlugin,
//replace exon with 5'UTR and add 3'UTR at same time.
}
}
});
}, this);
return allFeatures;
},
},

/**
* Title: _isSingle
Expand All @@ -524,19 +559,19 @@ return declare( JBrowsePlugin,
* @param {feature(Object)}
* @returns {feature(Object)}
*/
_isSingle: function(top_feat) {
_isSingle: function(top_feat) {
//console.log("Calling isSingle"); //TWS DEBUG

var initial_subf = top_feat.get('subfeatures');
var threeLevels = initial_subf.some(function(sf) {
return sf.get('subfeatures'); //If any subfeatures have subfeatures
});
return sf.get('subfeatures'); //If any subfeatures have subfeatures
});

var transcript_opts = initial_subf.map(function(sf, indx) {
var transcript_opts = initial_subf.map(function(sf, indx) {
//For populating selection menu
var sfName = sf.get('id') || sf.get('name') || sf.get('alias');
return {label: sfName, value: indx};
});
var sfName = sf.get('id') || sf.get('name') || sf.get('alias');
return {label: sfName, value: indx};
});

var deferredSelection = new Deferred();
//If threeLevels, resolve after dialog. Otherwise, resolve immediately
Expand Down