view misc/sscs_diff.py @ 18:e4d75f9efb90 draft

planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty

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

OPT_DEFAULTS = {}
USAGE = "%(prog)s [options]"
DESCRIPTION = """Find differences between the SSCS produced by one version of the pipeline and
another, when working on the same input MSA's."""
EPILOG = """Warning: This injects raw command-line arguments into shell commands and executes them.
"""


def main(argv):

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

  parser.add_argument('sscs_before', metavar='sscs.all.before.fa',
    help='SSCSs from earlier version (can be gzipped).')
  parser.add_argument('sscs_after', metavar='sscs.all.after.fa',
    help='SSCSs from later version (can be gzipped).')
  parser.add_argument('-b', '--before', metavar='sscs.all.before.diffs.fa', required=True,
    help='Output SSCSs from earlier version that differ from the SSCS in the later version here.')
  parser.add_argument('-a', '--after', metavar='sscs.all.after.diffs.fa', required=True,
    help='Output SSCSs from later version that differ from the SSCS in the earlier version here.')

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

  sscs_before = {}
  if args.sscs_before.endswith('.gz'):
    command = 'gunzip -c {} | paste - - | sort'.format(args.sscs_before)
  else:
    command = 'cat {} | paste - - | sort'.format(args.sscs_before)
  process = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE)
  for line in process.stdout:
    fields = line.rstrip('\r\n').split('\t')
    name = fields[0].lstrip('>').split()[0]
    seq = fields[1]
    sscs_before[name] = seq

  before_fh = open(args.before, 'w')
  after_fh = open(args.after, 'w')
  diffs = {}
  if args.sscs_after.endswith('.gz'):
    command = 'gunzip -c {} | paste - - | sort'.format(args.sscs_after)
  else:
    command = 'cat {} | paste - - | sort'.format(args.sscs_after)
  process = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE)
  for line in process.stdout:
    fields = line.rstrip('\r\n').split('\t')
    header = fields[0].lstrip('>')
    name, fam_size = header.split()
    seq_after = fields[1]
    if name in sscs_before:
      seq_before = sscs_before[name]
      if seq_before != seq_after:
        diffs[name] = (seq_before, seq_after)
        before_fh.write('>{} {}\n'.format(name, fam_size))
        before_fh.write(seq_before+'\n')
        after_fh.write('>{} {}\n'.format(name, fam_size))
        after_fh.write(seq_after+'\n')
  before_fh.close()
  after_fh.close()


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


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