6 from htsworkflow.pipelines.eland import extract_eland_sequence
9 usage = "usage: %prog [options] infile [outfile]"
11 parser = optparse.OptionParser(usage)
12 parser.add_option("-e", "--extract", dest="slice",
14 help="provide a python slice operator to select a portion of an eland file")
18 parser = make_parser()
20 (opt, args) = parser.parse_args(argv)
22 if len(args) not in (0, 1, 2):
23 parser.error('incorrect number of arguments')
25 # get our slice coordinates
26 start, end = opt.slice.split(':')
38 instream = open(args[0],'r')
43 outstream = open(args[1],'w')
45 outstream = sys.stdout
47 extract_eland_sequence(instream, outstream, start, end)
49 if __name__ == "__main__":
50 sys.exit(main(sys.argv[1:]))