#!/usr/bin/env python
import optparse
import os
import sys

from htsworkflow.pipelines.eland import extract_eland_sequence

def make_parser():
  usage = "usage: %prog [options] infile [outfile]"

  parser = optparse.OptionParser(usage)
  parser.add_option("-e", "--extract", dest="slice",
    default=":",
    help="provide a python slice operator to select a portion of an eland file")
  return parser

def main(argv):
  parser = make_parser()

  (opt, args) = parser.parse_args(argv)

  if len(args) not in (0, 1, 2):
    parser.error('incorrect number of arguments')

  # get our slice coordinates
  start, end = opt.slice.split(':')
  if len(start) > 0:
    start = int(start)
  else:
    start = None
  if len(end) > 0:
    end = int(end)
  else:
    end = None

  # open infile
  if len(args) > 0:
    instream = open(args[0],'r')
  else:
    instream = sys.stdin

  if len(args) > 1:
    outstream = open(args[1],'w')
  else:
    outstream = sys.stdout

  extract_eland_sequence(instream, outstream, start, end)

if __name__ == "__main__":
    sys.exit(main(sys.argv[1:]))