openbabel_remduplicates: subsearch.py annotate

annotate subsearch.py @ 12:8c4a4e9e173c draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"

author	bgruening
date	Tue, 28 Jul 2020 12:01:17 +0000
parents	112341e4fc94
children	d44de092fef3

rev	line source
0 112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	1 #!/usr/bin/env python
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	2 """
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	3 Input: Molecules in SDF, SMILES ...
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	4 Output: Moleculs filtered with specified substructures.
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	5 Copyright 2013, Bjoern Gruening and Xavier Lucas
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	6 """
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	7 import sys, os
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	8 import argparse
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	9 import multiprocessing
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	10 import tempfile
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	11 import subprocess
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	12 import shutil
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	13
12 8c4a4e9e173c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0" bgruening parents: 0 diff changeset	14 from openbabel import openbabel, pybel
8c4a4e9e173c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0" bgruening parents: 0 diff changeset	15 openbabel.obErrorLog.StopLogging()
8c4a4e9e173c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0" bgruening parents: 0 diff changeset	16
0 112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	17 def parse_command_line():
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	18 parser = argparse.ArgumentParser()
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	19 parser.add_argument('-i', '--infile', required=True, help='Molecule file.')
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	20 parser.add_argument('--iformat', help='Input format.')
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	21 parser.add_argument('--fastsearch-index', dest="fastsearch_index",
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	22 required=True, help='Path to the openbabel fastsearch index.')
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	23 parser.add_argument('-o', '--outfile', required=True, help='Path to the output file.')
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	24 parser.add_argument('--oformat',
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	25 default='smi', help='Output file format')
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	26 parser.add_argument("--max-candidates", dest="max_candidates", type=int,
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	27 default=4000, help="The maximum number of candidates.")
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	28 parser.add_argument('-p', '--processors', type=int,
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	29 default=multiprocessing.cpu_count())
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	30 return parser.parse_args()
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	31
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	32 results = list()
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	33 def mp_callback(res):
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	34 results.append(res)
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	35
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	36 def mp_helper( query, args ):
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	37 """
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	38 Helper function for multiprocessing.
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	39 That function is a wrapper around the following command:
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	40 obabel file.fs -s"smarts" -Ooutfile.smi -al 999999999
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	41 """
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	42
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	43 if args.oformat == 'names':
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	44 opts = '-osmi -xt'
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	45 else:
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	46 opts = '-o%s' % args.oformat
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	47
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	48 tmp = tempfile.NamedTemporaryFile(delete=False)
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	49 cmd = 'obabel -ifs %s -O %s %s -s%s -al %s' % (args.fastsearch_index, tmp.name, opts, query, args.max_candidates)
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	50
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	51 child = subprocess.Popen(cmd.split(),
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	52 stdout=subprocess.PIPE, stderr=subprocess.PIPE)
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	53
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	54 stdout, stderr = child.communicate()
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	55 return_code = child.returncode
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	56
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	57 if return_code:
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	58 sys.stdout.write(stdout)
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	59 sys.stderr.write(stderr)
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	60 sys.stderr.write("Return error code %i from command:\n" % return_code)
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	61 sys.stderr.write("%s\n" % cmd)
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	62 else:
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	63 sys.stdout.write(stdout)
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	64 sys.stdout.write(stderr)
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	65 return (tmp.name, query)
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	66
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	67
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	68 def get_smiles_or_smarts( args ):
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	69 """
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	70 Wrapper to retrieve a striped SMILES or SMARTS string from different input formats.
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	71 """
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	72 if args.iformat in ['smi', 'text', 'tabular']:
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	73 with open( args.infile ) as text_file:
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	74 for line in text_file:
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	75 yield line.split('\t')[0].strip()
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	76 else:
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	77 # inchi or sdf files
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	78 for mol in pybel.readfile( args.iformat, args.infile ):
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	79 yield mol.write('smiles').split('\t')[0]
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	80
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	81 def substructure_search( args ):
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	82
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	83 pool = multiprocessing.Pool( args.processors )
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	84 for query in get_smiles_or_smarts( args ):
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	85 pool.apply_async(mp_helper, args=(query, args), callback=mp_callback)
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	86 #mp_callback( mp_helper(query, args) )
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	87 pool.close()
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	88 pool.join()
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	89
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	90 if args.oformat == 'names':
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	91 out_handle = open( args.outfile, 'w' )
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	92 for result_file, query in results:
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	93 with open(result_file) as res_handle:
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	94 for line in res_handle:
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	95 out_handle.write('%s\t%s\n' % ( line.strip(), query ))
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	96 os.remove( result_file )
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	97 out_handle.close()
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	98 else:
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	99 out_handle = open( args.outfile, 'wb' )
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	100 for result_file, query in results:
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	101 res_handle = open(result_file,'rb')
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	102 shutil.copyfileobj( res_handle, out_handle )
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	103 res_handle.close()
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	104 os.remove( result_file )
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	105 out_handle.close()
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	106
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	107
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	108 def __main__():
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	109 """
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	110 Multiprocessing Open Babel Substructure Search.
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	111 """
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	112 args = parse_command_line()
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	113 substructure_search( args )
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	114
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	115 if __name__ == "__main__" :
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502 bgruening parents: diff changeset	116 __main__()

Mercurial > repos > bgruening > openbabel_remduplicates

annotate subsearch.py @ 12:8c4a4e9e173c draft