allpy: 6134ae1dfdae utils/pool

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view utils/pool @ 896:6134ae1dfdae

fix error caused by applying secondary structure markup This bug should be digged. For some reason BioPython's DSSP failed to get secondary structure information of a residue: $ ./pair_cores/pair_cores.py -i test/aln1.fasta -y aaa -e True ... ('A', (' ', 51, ' ')) caused by dssp.__getitem__

author	Boris Nagaev <bnagaev@gmail.com>
date	Fri, 23 Sep 2011 14:10:25 +0400
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1 #!/usr/bin/python

2 import subprocess

3 import os

4 import shlex

5 import optparse

7 p = optparse.OptionParser()

8 p.add_option('-n', '--size', type=int, help='Pool size')

9 p.add_option('-c', '--cmd',

10 help='Command template. Insert {} for argument.'

11 ' Put the argument in double quotes if it may contain spaces.')

12 options, args = p.parse_args()

14 spawned = 0

15 for arg in args:

16 if spawned > options.size:

17 os.wait()

18 spawned -= 1

19 cmd = shlex.split(options.cmd.replace('{}', arg))

20 subprocess.Popen(cmd)

21 spawned += 1

23 try:

24 while True:

25 os.wait()

26 except Exception:

27 pass

29 # vim: set ts=4 sts=4 et sw=4: