gff3.js

var $ = require('jquery');

module.exports = {
    process: function(gff3_data, types, longest) {
        var features = [];
        gff3_data.split('\n').map(function(line) {
            if (!line.startsWith('#') && line.length != 0) {
                var parts = line.split('\t');

                if (parts.length !== 9) {
                    //the file might use spaces instead of tabs
                    //ill try to split it by spaces
                    parts = line.trim().split(/\s+/);
                }

                if (parts.length == 9) {
                    var attParts = parts[8].split(';');
                    var arrayObject = {};
                    for (var i = 0; i < attParts.length; ++i) {
                        var pair = attParts[i].split("=");
                        arrayObject[pair[0]] = pair[1];
                    }

                    var feature = {
                        seqid: parts[0],
                        source: parts[1],
                        type: parts[2],
                        start: parseInt(parts[3]),
                        end: parseInt(parts[4]),
                        score: parts[5],
                        strand: parts[6],
                        phase: parts[7],
                        attributes: arrayObject
                    };
                    // check if user specified feature type
                    if (types === undefined || types.indexOf(feature.type) > -1) {
                        features.push(feature);
                    }
                } else { var err = new Error('9 parts of feature not found');
                    console.log(err);
                }
            }
        });
        return features;
    },
};