view test.py @ 4:af383638de66 draft

planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty

#!/usr/bin/env python
from __future__ import division
from __future__ import print_function
import sys
import argparse
import subprocess

OPT_DEFAULTS = {}
USAGE = "%(prog)s [options]"
DESCRIPTION = """"""


def main(argv):

  parser = argparse.ArgumentParser(description=DESCRIPTION)
  parser.set_defaults(**OPT_DEFAULTS)

  parser.add_argument('file1')
  parser.add_argument('file2')

  args = parser.parse_args(argv[1:])

  """
  cat $fastq1 | paste - - - - \
    | paste - <(cat $fastq2 | paste - - - -) \
    | awk -f make-barcodes.awk \
    | sort \
    | align_families.py \
    | duplex.py \
    > $sscs
  """

  cmd1 = subprocess.Popen(['cat', args.file1], stdout=subprocess.PIPE)
  cmd2 = subprocess.Popen(['cat', args.file2], stdout=subprocess.PIPE)


def fail(message):
  sys.stderr.write(message+"\n")
  sys.exit(1)

if __name__ == '__main__':
  sys.exit(main(sys.argv))