@gmod/jbrowse/src/JBrowse/Store/SeqFeature/BED/Parser.js

JBrowse - client-side genome browser

/* The function to parse the bed files. The standard BED file format (BED-6) is "chr\tstart(0based)\tEnd(1based)\tname\tscore\tstrand

BED-3 is the minimal parsed line by this parser (i.e. includes only first three fields)
Optional header lines start with '#'
*/
define( [
            'dojo/_base/declare',
            'dojo/_base/array',
            'dojo/_base/lang',
            'JBrowse/Util/TextIterator',
        ],
        function (
            declare,
            array,
            lang,
            TextIterator,
        ) {

var bed_feature_names = 'seq_id start end name score strand'.split(" ");

return declare( null, {

    constructor: function( args ) {
        lang.mixin( this, {
                        featureCallback:   args.featureCallback || function() {},
                        endCallback:       args.endCallback || function() {},
                        commentCallback:   args.commentCallback || function() {},
                        errorCallback:     args.errorCallback || function(e) { console.error(e); },
                        store:             args.store,
                        // if this is true, the parser ignores the
                        // rest of the lines in the file.  currently
                        // set when the file switches over to FASTA
                        eof: false
                    });
    },


    /**
     * Parse the bytes that contain the BED header, storing the parsed
     * data in this.header.
     */
    parseHeader: function( headerBytes ) {

        // parse the header lines
        var headData = {};
        var lineIterator = new TextIterator.FromBytes({ bytes: headerBytes });
        var line;
        while(( line = lineIterator.getline() )) {

            // only interested in meta and header lines
            if( line[0] != '#' )
                continue;

            // parse meta line using the parseHeader configuration callback function
            var metaData = (this.config.parseHeader||function() {})(line);
            var key = metaData.key;
            headData[key] = metaData.value;
        }

        this.header = headData;
        return headData;
    },
    finish: function() {
        this.endCallback();
    },
    addLine: function( line ) {
        var match;
        if( this.eof ) {
            // do nothing
        } else if( /^\s*[^#\s>]/.test(line) ) { //< feature line, most common case
            line = line.replace( /\r?\n?$/g, '' );
            var f = this.parse_feature( line );
            this.featureCallback( this._return_item([f]) );
        }
        // directive or comment
        else if(( match = /^\s*(\#+)(.*)/.exec( line ) )) {
            var hashsigns = match[1], contents = match[2];
            contents = contents.replace(/\s*/,'');
            this._return_item({ comment: contents });
        }
        else if( /^\s*$/.test( line ) ) {
            // blank line, do nothing
        }
        else if( /^\s*>/.test(line) ) {
            // implicit beginning of a FASTA section.  just stop
            // parsing, since we don't currently handle sequences
            this._return_all_under_construction_features();
            this.eof = true;
        }
        else { // it's a parse error
            line = line.replace( /\r?\n?$/g, '' );
            throw "GFF3 parse error.  Cannot parse '"+line+"'.";
        }
    },

    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 ) );
                            });
    },

    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 = {};
        for( var i = 0; i < bed_feature_names.length; i++ ) {
            if(f[i]) {
                parsed[ bed_feature_names[i] ] = 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;
    },

    _return_item: function(i) {
        if( i[0] )
            this.featureCallback( i );
        else if( i.comment )
            this.commentCallback( i, this.store );
    }

});
});