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Merge 6e9d314 into d36d5be
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@nathandunn
nathandunn committed Feb 11, 2019
2 parents d36d5be + 6e9d314 commit eac0bed
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Showing 3 changed files with 102 additions and 39 deletions.
131 changes: 94 additions & 37 deletions client/apollo/js/JSONUtils.js
View file
@@ -1,7 +1,7 @@
define([ 'dojo/_base/declare',
'dojo/_base/array',
'JBrowse/Util',
'JBrowse/Model/SimpleFeature',
'JBrowse/Model/SimpleFeature',
'WebApollo/SequenceOntologyUtils'
],
function( declare, array, Util, SimpleFeature, SeqOnto ) {
Expand Down Expand Up @@ -38,7 +38,7 @@ var JAFeature = declare( SimpleFeature, {
constructor: function( afeature, parent ) {
this.afeature = afeature;
if (parent) { this._parent = parent; }

// get the main data
var loc = afeature.location;
var pfeat = this;
Expand All @@ -49,21 +49,21 @@ var JAFeature = declare( SimpleFeature, {
name: afeature.name,
parent_id: afeature.parent_id,
parent_type: afeature.parent_type ? afeature.parent_type.name : undefined,
type: afeature.type.name,
type: afeature.type.name,
properties: afeature.properties
};

if (this.data.type === "CDS") {
this.data.type = "wholeCDS";
if (this.data.type === "CDS") {
this.data.type = "wholeCDS";
}
else if (this.data.type === "stop_codon_read_through") {
parent.data.readThroughStopCodon = true;
}

this._uniqueID = afeature.uniquename;

// this doesn't work, since can be multiple properties with same CV term (comments, for example)
// could create arrray for each flattened cv-name for multiple values, but not sure what the point would be over
// could create arrray for each flattened cv-name for multiple values, but not sure what the point would be over
// just making sure can access via get('properties') via above assignment into data object
// parse the props
/* var props = afeature.properties;
Expand Down Expand Up @@ -95,7 +95,7 @@ var JAFeature = declare( SimpleFeature, {
}
}
}

if (!parent) {
if (afeature.children) {
var descendants = [];
Expand All @@ -116,16 +116,16 @@ var JAFeature = declare( SimpleFeature, {
afeature.children = [ child ];
}
}

// moved subfeature assignment to bottom of feature construction, since subfeatures may need to call method on their parent
// only thing subfeature constructor won't have access to is parent.data.subfeatures
// get the subfeatures
// get the subfeatures
this.data.subfeatures = array.map( afeature.children, function(s) {
return new JAFeature( s, pfeat);
} );

},

getUniqueName: function() {
if (this.parent() && this.parent().get("cloned_subfeatures")) {
return this.parent().id();
Expand All @@ -152,18 +152,18 @@ JSONUtils.flattenFeature = function(feature, descendants) {


/**
* takes any JBrowse feature, returns a SimpleFeature "copy",
* takes any JBrowse feature, returns a SimpleFeature "copy",
* for which all properties returned by tags() are mutable (has set() method)
* needed since JBrowse features no longer necessarily mutable
* feature requirements:
* functions: id, parent, tags, get
* if subfeatures, then returned as array by feature.get('subfeatures')
*
*
*/
JSONUtils.makeSimpleFeature = function(feature, parent) {
var result = new SimpleFeature({id: feature.id(), parent: (parent ? parent : feature.parent()) });
var ftags = feature.tags();
for (var tindex = 0; tindex < ftags.length; tindex++) {
for (var tindex = 0; tindex < ftags.length; tindex++) {
var tag = ftags[tindex];
// forcing lower case, since still having case issues with NCList features
result.set(tag.toLowerCase(), feature.get(tag.toLowerCase()));
Expand All @@ -187,7 +187,7 @@ JSONUtils.makeSimpleFeature = function(feature, parent) {
* afeature: sequence alteration in ApolloEditorService JSON format,
*/
JSONUtils.createJBrowseSequenceAlteration = function( afeature ) {
var loc = afeature.location;
var loc = afeature.location;
var uid = afeature.uniquename;
var justification;
for (var i = 0; i < afeature.properties.length; i++) {
Expand All @@ -212,42 +212,99 @@ JSONUtils.createJBrowseSequenceAlteration = function( afeature ) {
};


/**
JSONUtils.handleCigarSubFeatures = function(feature,type){
type = type ? type : feature.get('type');
if(type.endsWith('RNA') && JSONUtils.isAlignment(feature)){
feature = JSONUtils.generateSubFeaturesFromCigar(feature)
}
return feature ;
};

JSONUtils.isAlignment = function(feature){
try {
return feature.data.cigar !== undefined;
} catch (e) {
console.error('Unable to process feature alignment. Assuming not an alignment',feature,e);
return false;
}
};

JSONUtils.parseCigar = function( cigar ) {
return array.map( cigar.toUpperCase().match(/\d+\D/g), function( op ) {
return [ op.match(/\D/)[0], parseInt( op ) ];
});
};

/**
* Generate exon subfeatures only from M vs N.
* @param feature
*/
JSONUtils.generateSubFeaturesFromCigar = function(feature){
var cigarData = feature.data.cigar ;
// 12M3N5M9N4M
// split <Number>Cigar
var ops = this.parseCigar(cigarData);
var currOffset = 0;
console.log('ffeature',feature);
var start = feature.data.start ;
// var featureToAdd = JSONUtils.makeSimpleFeature(feature);
feature.set('subfeatures', []);
array.forEach( ops, function( oprec ) {
var op = oprec[0];
var len = oprec[1];
if( op === 'M' || op === '=' || op === 'E' ) {
// create an exon subfeature for each
// add subfeature
var exon = new SimpleFeature({parent:feature});
exon.set('start', currOffset+start);
exon.set('end', currOffset + len+start);
exon.set('strand', feature.strand);
exon.set('type', 'exon');
var subfeature = JSONUtils.makeSimpleFeature(exon,feature);
feature.get("subfeatures").push(subfeature);
}
currOffset += len;
});
return feature;
};

/**
* creates a feature in ApolloEditorService JSON format
* takes as argument:
* jfeature: a feature in JBrowse JSON format,
* jfeature: a feature in JBrowse JSON format,
* fields: array specifying order of fields in jfeature
* subfields: array specifying order of fields in subfeatures of jfeature
* specified_type (optional): type passed in that overrides type info for jfeature
* ApolloEditorService format:
* {
* "location" : { "fmin": fmin, "fmax": fmax, "strand": strand },
* {
* "location" : { "fmin": fmin, "fmax": fmax, "strand": strand },
* "type": { "cv": { "name":, cv }, // typical cv name: "SO" (Sequence Ontology)
* "name": cvterm }, // typical name: "transcript"
* "children": { __recursive ApolloEditorService feature__ }
* }
*
* For ApolloEditorService "add_feature" call to work, need to have "gene" as toplevel feature,
*
* For ApolloEditorService "add_feature" call to work, need to have "gene" as toplevel feature,
* then "transcript", then ???
*
*
* JBrowse JSON fields example: ["start", "end", "strand", "id", "subfeatures"]
*
* type handling
* if specified_type arg present, it determines type name
* else if fields has a "type" field, use that to determine type name
* else don't include type
* else don't include type
*
* ignoring JBrowse ID / name fields for now
* currently, for features with lazy-loaded children, ignores children
* currently, for features with lazy-loaded children, ignores children
*/
JSONUtils.createApolloFeature = function( jfeature, specified_type, useName, specified_subtype ) {
console.log('creating apollo feature',jfeature);
var diagnose = (JSONUtils.verbose_conversion && jfeature.children() && jfeature.children().length > 0);
if (diagnose) {
console.log("converting JBrowse feature to Apollo feture, specified type: " + specified_type);
if (diagnose) {
console.log("converting JBrowse feature to Apollo feture, specified type: " + specified_type);
console.log(jfeature);
}

var afeature = new Object();
var afeature = {};
var astrand;
// Apollo feature strand must be an integer
// either 1 (plus strand), -1 (minus strand), or 0? (not stranded or strand is unknown?)
Expand All @@ -261,7 +318,7 @@ JSONUtils.createApolloFeature = function( jfeature, specified_type, useName, spe
default:
astrand = 0; // either not stranded or strand is uknown
}

afeature.location = {
"fmin": jfeature.get('start'),
"fmax": jfeature.get('end'),
Expand Down Expand Up @@ -295,7 +352,7 @@ JSONUtils.createApolloFeature = function( jfeature, specified_type, useName, spe
// using 'id' attribute in the absence of 'name' attribute
name !== undefined ? afeature.name = name : afeature.name = id;
}

/*
afeature.properties = [];
var property = { value : "source_id=" + jfeature.get('id'),
Expand All @@ -314,14 +371,14 @@ JSONUtils.createApolloFeature = function( jfeature, specified_type, useName, spe
// use filteredsubs if present instead of subfeats?
// if (jfeature.filteredsubs) { subfeats = jfeature.filteredsubs; }
// else { subfeats = jfeature.get('subfeatures'); }
subfeats = jfeature.get('subfeatures');
subfeats = jfeature.get('subfeatures');
if( subfeats && subfeats.length ) {
afeature.children = [];
var slength = subfeats.length;
var cds;
var cdsFeatures = [];
var foundExons = false;

var updateCds = function(subfeat) {
if (!cds) {
cds = new SimpleFeature({id: "cds", parent: jfeature});
Expand All @@ -339,14 +396,14 @@ JSONUtils.createApolloFeature = function( jfeature, specified_type, useName, spe
}
}
};

for (var i=0; i<slength; i++) {
var subfeat = subfeats[i];
var subtype = subfeat.get('type');
var converted_subtype = specified_subtype || subtype;
if (!specified_subtype) {
if (SeqOnto.exonTerms[subtype]) {
// definitely an exon, leave exact subtype as is
// definitely an exon, leave exact subtype as is
// converted_subtype = "exon"
}
else if (subtype === "wholeCDS" || subtype === "polypeptide") {
Expand All @@ -361,7 +418,7 @@ JSONUtils.createApolloFeature = function( jfeature, specified_type, useName, spe
converted_subtype = null;
cdsFeatures.push(subfeat);
}
else if (SeqOnto.spliceTerms[subtype]) {
else if (SeqOnto.spliceTerms[subtype]) {
// splice sites -- filter out? leave unchanged?
// 12/16/2012 filtering out for now, causes errors in AnnotTrack duplication operation
converted_subtype = null; // filter out
Expand All @@ -379,7 +436,7 @@ JSONUtils.createApolloFeature = function( jfeature, specified_type, useName, spe
// filter out UTR
converted_subtype = null;
}
else {
else {
// convert everything else to exon???
// need to do this since server only creates exons for "exon" and descendant terms
converted_subtype = "exon";
Expand All @@ -406,7 +463,7 @@ JSONUtils.createApolloFeature = function( jfeature, specified_type, useName, spe
}
}
else if ( specified_type === 'transcript' ) {
// special casing for Apollo "transcript" features being created from
// special casing for Apollo "transcript" features being created from
// JBrowse top-level features that have no children
// need to create an artificial exon child the same size as the transcript
var fake_exon = new SimpleFeature({id: jfeature.id()+"_dummy_exon", parent: jfeature});
Expand Down Expand Up @@ -595,5 +652,5 @@ JSONUtils.classifyVariant = function( refAllele, altAlleles, fmin, fmax ) {
window.JSONUtils = JSONUtils;

return JSONUtils;

});
2 changes: 2 additions & 0 deletions client/apollo/js/View/Track/AnnotTrack.js
View file
Expand Up @@ -1100,6 +1100,7 @@ define([
var keys = Object.keys(parentFeatures);
var singleParent = keys.length === 1;
var featureToAdd;
console.log('preccing new feature',parentFeatures)
if (singleParent) {
featureToAdd = JSONUtils.makeSimpleFeature(parentFeatures[keys[0]]);
}
Expand Down Expand Up @@ -1169,6 +1170,7 @@ define([
}

var afeat ;
featureToAdd = JSONUtils.handleCigarSubFeatures(featureToAdd,biotype);
if(biotype === 'mRNA'){
afeat = JSONUtils.createApolloFeature(featureToAdd, biotype, true);
featuresToAdd.push(afeat);
Expand Down
8 changes: 6 additions & 2 deletions client/apollo/js/View/Track/DraggableHTMLFeatures.js
View file
Expand Up @@ -15,7 +15,8 @@ define( [
'dijit/Dialog',
'JBrowse/Util',
'JBrowse/Model/SimpleFeature',
'WebApollo/SequenceOntologyUtils'
'WebApollo/SequenceOntologyUtils',
'WebApollo/JSONUtils',
],
function( declare,
array,
Expand All @@ -29,7 +30,9 @@ define( [
dijitDialog,
Util,
SimpleFeature,
SeqOnto ) {
SeqOnto,
JSONUtils
) {

var debugFrame = false ;

Expand Down Expand Up @@ -1201,6 +1204,7 @@ var draggableTrack = declare( HTMLFeatureTrack,
onClick: dojo.hitch(this, function() {
var selection = this.selectionManager.getSelection();
this.selectionManager.clearSelection();
selection = JSONUtils.handleCigarSubFeatures(selection,'mRNA');
atrack.createAnnotations(selection,true);
})
}));
Expand Down

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