kolodny-vs-gallant

#!/usr/bin/env python2.7

import os
import re
import sys

import pybcb as bcb
import pybcb.flags as flags

flags.use_all('pdb-dir', 'tmp-dir', 'results-dir', 'ignore-cache', 'no-cache',
              'frag-lib')
flags.use('old-fragbag', (
    lambda: flags.add(dest='old_fragbag', type=str,
                      help='The old FragBag executable.'),
    flags.verify_path,
))
flags.use('frag-brk-lib', (
    lambda: flags.add(dest='frag_brk_lib', type=str,
                      help='An origin brk fragment library file.'),
    flags.verify_path,
))
flags.use('pdbids', (
    lambda: flags.add(dest='pdbids', type=str,
                      help='A file containing PDB ids, one per line.'),
    flags.verify_path,
))
flags.init()

exp_dirname = os.path.basename(flags.config.pdbids)
results_dirname = exp_dirname

exp_dir = os.path.join(flags.config.tmp_dir, exp_dirname)
results_dir = os.path.join(flags.config.results_dir, results_dirname)

bcb.make()
bcb.set_exp_dir(exp_dir)
bcb.set_results_dir(results_dir)

gzpdbfiles = map(str.strip, list(open(flags.config.pdbids).readlines()))
pdbfiles = []

# The old fragbag can't handle gzipped PDB files...
for pdbgz in gzpdbfiles:
    if pdbgz.endswith('.gz'):
        pdbf = bcb.ejoin(os.path.basename(re.sub('\.gz$', '', pdbgz)))
        print >> open(pdbf, 'w+'), bcb.cmd('gunzip', '-c', pdbgz)
        pdbfiles.append(pdbf)
    else:
        pdbfiles.append(pdbgz)

concat_file = bcb.rjoin('concat-chains')
def oldstyle():
    w = open(concat_file, 'w+')
    print >> w, bcb.cmd('diff-kolodny-fragbag', '--oldstyle',
                        '--fragbag', flags.config.old_fragbag,
                        flags.config.frag_lib,
                        flags.config.frag_brk_lib,
                        *pdbfiles)
    w.close()
bcb.cached([concat_file], oldstyle)

separate_file = bcb.rjoin('separate-chains')
def newstyle():
    w = open(separate_file, 'w+')
    print >> w, bcb.cmd('diff-kolodny-fragbag',
                        '--fragbag', flags.config.old_fragbag,
                        flags.config.frag_lib,
                        flags.config.frag_brk_lib,
                        *pdbfiles)
    w.close()
bcb.cached([separate_file], newstyle)