#!/usr/bin/env python

from __future__ import print_function, division, unicode_literals

__doc__ = """filter geneinfo files by given criteria"""

import argparse
import os
import sys

import uta.formats.geneinfo as ufgi


def parse_args(argv):
    ap = argparse.ArgumentParser(
        description=__doc__,
        )
    ap.add_argument(
        'FILE'
        )
    ap.add_argument(
        '--genes-from', '-G',
        )
    
    opts = ap.parse_args(argv)
    return opts


if __name__ == '__main__':
    opts = parse_args(sys.argv[1:])

    filter_genes = set()
    if opts.genes_from:
        filter_genes = set([ l.strip() for l in open(opts.genes_from,'r').readlines() ])

    gir = ufgi.GeneInfoReader(sys.stdin if opts.FILE == '-' else open(opts.FILE,'r'))
    giw = ufgi.GeneInfoWriter(sys.stdout)

    for gi in gir:
        if gi.hgnc in filter_genes:
            giw.write(gi)
