1.1 --- a/pair_cores/pair_cores_all.py	Wed Jul 13 17:14:42 2011 +0200
     1.2 +++ b/pair_cores/pair_cores_all.py	Wed Jul 13 17:29:52 2011 +0200
     1.3 @@ -47,7 +47,19 @@
     1.4  def homology_from_markup_all(input_dir, output_dir, max_delta,
     1.5          markups_list=None, alignments_list=None,
     1.6          suffix=".homology.xls", pdb_getter=cached_download_pdb, cpu_count=0):
     1.7 -    """ FIXME """
     1.8 +    """ Run pair_cores in parallel
     1.9 +
    1.10 +    * input_dir -- directory with input files (alignments or markups)
    1.11 +    * output_dir -- directory where output files will be written
    1.12 +    * max_delta -- see geometrical_cores method from structure module
    1.13 +    * markups_list -- list of names of input markup files
    1.14 +    * alignments_list -- list of names of input alignment files
    1.15 +      Note: do not use both markups_list and alignments_list.
    1.16 +      The type of these arguments should be a list of file names
    1.17 +      or up to MAX_GLOBS glogs relative to input_dir.
    1.18 +    * suffix -- string, appending to name of output file
    1.19 +    * cpu_count -- number of parallel workers (0 means number of CPUs)
    1.20 +    """
    1.21      if markups_list:
    1.22          files = resolve_globs(input_dir, markups_list)
    1.23          func = homology_from_markup
    1.24 @@ -83,7 +95,7 @@
    1.25      p.add_argument('-d',help='Distance spreading',metavar='float',type=float,default=2.0)
    1.26      p.add_argument('-s',help='Suffix added to names of output files',metavar='STR',type=str,default=".homology.xls")
    1.27      p.add_argument('-c',help='Pdb cache directory',metavar='DIR',type=str, default='pdb_cache')
    1.28 -    p.add_argument('-j',help='Number of workers',metavar='INT',type=int, default=2)
    1.29 +    p.add_argument('-j',help='Number of workers (0 means number of CPUs)',metavar='INT',type=int, default=2)
    1.30      args = p.parse_args()
    1.31      homology_from_markup_all(input_dir=args.i, output_dir=args.o, max_delta=args.d,
    1.32          markups_list=args.l, alignments_list=args.a,