1.1 --- /dev/null	Thu Jan 01 00:00:00 1970 +0000
     1.2 +++ b/pair_cores/against-database.py	Wed Oct 26 22:44:07 2011 +0300
     1.3 @@ -0,0 +1,85 @@
     1.4 +#!/usr/bin/python
     1.5 +
     1.6 +import os
     1.7 +import glob
     1.8 +import warnings
     1.9 +import argparse
    1.10 +import multiprocessing as mp
    1.11 +
    1.12 +from pair_cores_all import homology_from_markup_all
    1.13 +score_all = __import__('score-all').score_all
    1.14 +from allpy.homology import MonomerHomology as MH
    1.15 +from allpy.util import Binder
    1.16 +from allpy.structure import CachedDownloadPdb
    1.17 +
    1.18 +def makedirs(d):
    1.19 +    try:
    1.20 +        os.makedirs(d)
    1.21 +    except:
    1.22 +        pass
    1.23 +
    1.24 +def case_homology(file_in, file_out, case):
    1.25 +    MH.case_homology(file_in, file_out, case, 'markup')
    1.26 +
    1.27 +def against_database(markups_dir, mask, output_dir, scores, delta, cache,
    1.28 +        jobs, pair_cores, case, no_case, suffix):
    1.29 +    makedirs(output_dir)
    1.30 +    makedirs(os.path.join(output_dir, pair_cores))
    1.31 +    makedirs(os.path.join(output_dir, case))
    1.32 +    makedirs(os.path.join(output_dir, no_case))
    1.33 +    case_tasks = []
    1.34 +    for f in glob.glob(os.path.join(markups_dir, mask)):
    1.35 +        f = os.path.basename(f)
    1.36 +        case_tasks.append(Binder(case_homology,
    1.37 +            os.path.join(markups_dir, f),
    1.38 +            os.path.join(output_dir, case, f+suffix), True))
    1.39 +        case_tasks.append(Binder(case_homology,
    1.40 +            os.path.join(markups_dir, f),
    1.41 +            os.path.join(output_dir, no_case, f+suffix), False))
    1.42 +    jobs = jobs or mp.cpu_count()
    1.43 +    mp.Pool(processes=jobs).map(apply, case_tasks)
    1.44 +
    1.45 +    homology_from_markup_all(input_dir=markups_dir,
    1.46 +        output_dir=os.path.join(output_dir, pair_cores), max_delta=delta,
    1.47 +        markups_list=mask, suffix=suffix,
    1.48 +        pdb_getter=CachedDownloadPdb(cache_dir=cache), cpu_count=jobs)
    1.49 +
    1.50 +    score_all(output_dir, pair_cores, case, no_case, mask+suffix, scores)
    1.51 +
    1.52 +def main():
    1.53 +    p = argparse.ArgumentParser(description='PairCores. ScoreAll',
    1.54 +        formatter_class=argparse.ArgumentDefaultsHelpFormatter)
    1.55 +    p.add_argument('-i', '--markups-dir', required=True,
    1.56 +            help='Directory with input markups')
    1.57 +    p.add_argument('-o', '--output-dir', required=True,
    1.58 +            help='Output directory')
    1.59 +    p.add_argument('-s', '--scores', type=argparse.FileType('w'), required=True,
    1.60 +            help='Output file with scores (final result)')
    1.61 +    p.add_argument('-m', '--mask', default='*.markup',
    1.62 +            help='Mask for input markup files in markups directory')
    1.63 +    p.add_argument('-d', '--delta', type=float, default=2.0,
    1.64 +            help='Distance spreading', )
    1.65 +    p.add_argument('-c', '--cache', default='pdb_cache',
    1.66 +            help='Pdb cache directory')
    1.67 +    p.add_argument('-j', '--jobs', type=int, default=0,
    1.68 +            help='Number of workers (0 means number of CPUs)')
    1.69 +    p.add_argument('--pair-cores', default='pair-cores',
    1.70 +            help='Pair-cores results subdirectory')
    1.71 +    p.add_argument('--case', default='case',
    1.72 +            help='Homology from alignment (taking into account letter case)')
    1.73 +    p.add_argument('--no-case', default='no-case',
    1.74 +            help='Homology from alignment (ignoring letter case)')
    1.75 +    p.add_argument('--suffix', default=".xls",
    1.76 +            help='Suffix added to names of homology files')
    1.77 +    a = p.parse_args()
    1.78 +    against_database(markups_dir=a.markups_dir, mask=a.mask,
    1.79 +        output_dir=a.output_dir, scores=a.scores, delta=a.delta, cache=a.cache,
    1.80 +        jobs=a.jobs, pair_cores=a.pair_cores, case=a.case, no_case=a.no_case,
    1.81 +        suffix=a.suffix)
    1.82 +
    1.83 +if __name__ == '__main__':
    1.84 +    try:
    1.85 +        main()
    1.86 +    except Exception, e:
    1.87 +        warnings.warn(str(e), stacklevel=2)
    1.88 +