muscle_node/muscle_driver.js

node.js wrapper for MUSCLE alignment

//import functions from muscle file
var muscle = require('./muscle.js');
//collect input file
var inFile = process.argv[2];
//get Path for input and output
var myfilePath = inFile;
var outFile = './Output/Result.aln';


//run muscle program
//if a folder named 'Output' does not exist, it will be created
//result will be places in 'Output' folder and saved as 'Result'
muscle.muscle_align(myfilePath, outFile, process.argv, muscle.align);


/*
****Basic usage 

    node muscle_driver.js <inputfile> [insert any flags preceeded by '-' sign and seperated by a space (from flags below)]
    
    e.g. node muscle_driver.js DNA.fasta -msf -html
    
    Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32(5):1792-1797. 

    Edgar, R.C. (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics, (5) 113. 
    
****Other flags

    -diags             Find diagonals (faster for similar sequences)
    -html              Write output in HTML format (default FASTA)
    -msf               Write output in GCG MSF format (default FASTA)
    -clw               Write output in CLUSTALW format (default FASTA)
    -clwstrict         As -clw, with 'CLUSTAL W (1.81)' header
    -quiet             Do not write progress messages to stderr
    
    */