merge.js

merge.js

#!/usr/local/bin/node

var fs = require('fs');
var data = fs.readFileSync(process.argv[2]);
var target = fs.readFileSync(process.argv[3]);

var lines = (data+'').split('\n');
var rows = (target+'').split('\n');

var row = 0;
console.log(rows[0]);
for (var i = 0; i < lines.length; i += 1) {
  var line = lines[i];
  if (line === '') {
    row += 1;
    console.log(rows[row]);
    continue;
  }
  if (line.split('\t')[1].split(' ').slice(2).length && line.split('\t')[2] === 'NA') {
    line = line.split('\t');
    line = line[0]+'\t'+line[1].split(' ').slice(0,2).join(' ')+'\t'+line[1].split(' ').slice(2).join(' ')+'\t'+line.slice(3).join('\t');
  }
  if (line.split('\t')[3].slice(0,1) !== '$') throw 'oh noes';
//  if (rows[row] === undefined) {console.log(row, rows[row], i, line);return}
  if (rows[row].split('\t').slice(1,3).join('\t').toUpperCase() !== line.split('\t').slice(0,2).join('\t')) {
    row += 1;
    console.log(rows[row]);
  }
  line = line.split('\t');
  console.log('\t'+line[0]+'\t'+line[1]+'\t\''+line[2]+'\t'+line.slice(3).join('\t'));
}