fasta_format_for_cpt.js

const fs = require('fs');
const sh = require('shelljs');

const indir = process.argv[2];
let iLineLength = Number(process.argv[3]);
let complementRerverse = process.argv[4];

iLineLength = (iLineLength) ? iLineLength : 80;

let infiles = sh.ls(indir + '/*_Cp.fa.formated.fa');

for(let infile of infiles){
  //console.log(infile);
  let ids = infile.match(/\/(\S+)\_Cp*\.fa/);
  //console.log(ids[1])

  let lines = fs.readFileSync(infile).toString().split(">");

  let seqObj = [];
  let seqObjObject = {};
  //let totalLength = 0;
  for(let i=1; i<lines.length; i++){
    //console.log(lines[i]);
    //let id = lines[i].split("\n")[0].split(/\s+/)[0];
    let id = ids[1] + "_Cp_" + i;

    //console.log(id);
    let seqOriginal = lines[i].split("\n").slice(1).join('');
    let seq = seqOriginal.replace(/\s+/g, '').toUpperCase().replace(/[^A|T|C|G]/g, 'N');
    //console.log(id + "\t" + seq.length);
    //totalLength += seq.length;
    seqObj.push([id, seq, seq.length]);
  }

  seqObj.sort(function(a, b){
    return b[2] - a[2];
  });

  let outfile = `${ids[1]}_Cp.fa`;
  for(let i=0; i<seqObj.length; i++){
    //console.log(">" + seqObj[i][0] + "\t" + seqObj[i][1] + "\n" + seqObj[i][2]);

    //process.stdout.write(fasta_print(seqObj[i][0], seqObj[i][1]));
    fs.writeFileSync(outfile, fasta_print(seqObj[i][0], seqObj[i][1]))


    //if (complementRerverse){
    //  let complementSequence = complement_seq(seqObj[i][1])
    //  process.stdout.write(fasta_print(seqObj[i][0] + '_complement', complementSequence));
    //}
  }
}

function complement_seq(seq){
  function complement(base){
    return {A : 'T', T: 'A', G: 'C', C: 'G' }[base];
  }

  let compSeq = seq.toUpperCase().split('').reverse().map(complement).join('');
  return compSeq;
}

function fasta_print(id, seq){
  let output = ">" + id + "\n";

  for (let i=0; i<seq.length; i +=iLineLength){
    output += seq.substr(i, iLineLength).toUpperCase() + "\n";
  }
  //console.log(output);
  return output;
}