muscle_node/muscle.js

node.js wrapper for MUSCLE alignment

//export functions below
var exports = module.exports = {};
//module for spawning new shell
var exec = require('child_process').exec;
//other flags will be pushed into otherlfags arr
var otherflags = [];


exports.muscle_align = function (myfilePath, outFile, flagArr, callback) {
    //check that enough arguments are supplied
    if (process.argv.length >= 3) {
        //generate commandline
        var mkDirCommand = 'mkdir Output';
        console.log('\n' + ' made Output folder...');
        //spawn child process for new shell command
        var child = exec(mkDirCommand, function (error, stdout, stderr) {
            if (error != null) {
                console.log(stderr);
            }
        });
        //invoke callback and push in arguments
        callback(myfilePath, outFile, flagArr);
    } else {
        console.log('insufficient number of arguments');
    }
}

exports.align = function (myfilePath, outFile, flagArr) {
    //merge other flags from commandline into a single string
    for (var i = 3; i < flagArr.length; i++) {
        otherflags.push(flagArr[i]);
    }
    //stringify
    var stringify = otherflags.toString();
    //replace commas with spaces
    var flags = stringify.replace(/,/g, " ");
    //generate the commandline 
    var alignCommand = 'muscle -in ' + myfilePath + ' -out ' + outFile + ' ' + flags;
    console.log('\n' + ' running...');
    //spawn child to run exec shell
    var child = exec(alignCommand, function (error, stdout, stderr) {
        if (error != null) {
            console.log(stderr);
        }
        console.log('\n' + ' finished!');
    });
}