allpy
annotate 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 |
| parents | |
| children |
| rev | line source |
|---|---|
| dendik@799 | 1 #!/usr/bin/python |
| dendik@799 | 2 import subprocess |
| dendik@799 | 3 import os |
| dendik@799 | 4 import shlex |
| dendik@799 | 5 import optparse |
| dendik@799 | 6 |
| dendik@799 | 7 p = optparse.OptionParser() |
| dendik@799 | 8 p.add_option('-n', '--size', type=int, help='Pool size') |
| dendik@799 | 9 p.add_option('-c', '--cmd', |
| dendik@799 | 10 help='Command template. Insert {} for argument.' |
| dendik@799 | 11 ' Put the argument in double quotes if it may contain spaces.') |
| dendik@799 | 12 options, args = p.parse_args() |
| dendik@799 | 13 |
| dendik@799 | 14 spawned = 0 |
| dendik@799 | 15 for arg in args: |
| dendik@799 | 16 if spawned > options.size: |
| dendik@799 | 17 os.wait() |
| dendik@799 | 18 spawned -= 1 |
| dendik@799 | 19 cmd = shlex.split(options.cmd.replace('{}', arg)) |
| dendik@799 | 20 subprocess.Popen(cmd) |
| dendik@799 | 21 spawned += 1 |
| dendik@799 | 22 |
| dendik@799 | 23 try: |
| dendik@799 | 24 while True: |
| dendik@799 | 25 os.wait() |
| dendik@799 | 26 except Exception: |
| dendik@799 | 27 pass |
| dendik@799 | 28 |
| dendik@799 | 29 # vim: set ts=4 sts=4 et sw=4: |