Mercurial > repos > bgruening > openbabel_filter

annotate multi_obgrep.py @ 14:8ee975c49a3d draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
author bgruening
date Mon, 19 Oct 2020 14:41:44 +0000
parents ff2dd4b7d918
children 988085c7a0ea
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1 #!/usr/bin/env python
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2 """
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3 Input: Molecules in SDF, SMILES ...
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4 Output: Molecule file filtered with obgrep.
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5 Copyright 2013, Bjoern Gruening and Xavier Lucas
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6 """
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7 import argparse
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8 import multiprocessing
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9 import os
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10 import shlex
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11 import shutil
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12 import subprocess
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13 import tempfile
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14
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16 def parse_command_line():
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17 parser = argparse.ArgumentParser()
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18 parser.add_argument('-i', '--infile', required=True, help='Molecule file.')
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19 parser.add_argument('-q', '--query', required=True, help='Query file, containing different SMARTS in each line.')
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20 parser.add_argument('-o', '--outfile', required=True, help='Path to the output file.')
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21 parser.add_argument("--iformat", help="Input format, like smi, sdf, inchi")
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22 parser.add_argument("--n-times", dest="n_times", type=int,
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23 default=0, help="Print a molecule only if the pattern occurs # times inside the molecule.")
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24 parser.add_argument('-p', '--processors', type=int, default=multiprocessing.cpu_count())
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25 parser.add_argument("--invert-matches", dest="invert_matches", action="store_true",
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26 default=False, help="Invert the matching, print non-matching molecules.")
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27 parser.add_argument("--only-name", dest="only_name", action="store_true",
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28 default=False, help="Only print the name of the molecules.")
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29 parser.add_argument("--full-match", dest="full_match", action="store_true",
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30 default=False, help="Full match, print matching-molecules only when the number of heavy atoms is also equal to the number of atoms in the SMARTS pattern.")
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31 parser.add_argument("--number-of-matches", dest="number_of_matches", action="store_true",
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32 default=False, help="Print the number of matches.")
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33 return parser.parse_args()
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36 results = list()
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39 def mp_callback(res):
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40 results.append(res)
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43 def mp_helper(query, args):
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44 """
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45 Helper function for multiprocessing.
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46 That function is a wrapper around obgrep.
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47 """
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49 cmd_list = []
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50 if args.invert_matches:
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51 cmd_list.append('-v')
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52 if args.only_name:
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53 cmd_list.append('-n')
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54 if args.full_match:
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55 cmd_list.append('-f')
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56 if args.number_of_matches:
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57 cmd_list.append('-c')
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58 if args.n_times:
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59 cmd_list.append('-t %s' % str(args.n_times))
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61 tmp = tempfile.NamedTemporaryFile(delete=False)
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62 cmd = 'obgrep %s "%s" %s' % (' '.join(cmd_list), query, args.infile)
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63 child = subprocess.Popen(shlex.split(cmd), stdout=open(tmp.name, 'w+'), stderr=subprocess.PIPE)
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65 stdout, stderr = child.communicate()
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66 return (tmp.name, query)
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69 def obgrep(args):
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70 temp_file = tempfile.NamedTemporaryFile()
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71 temp_link = "%s.%s" % (temp_file.name, args.iformat)
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72 temp_file.close()
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73 os.symlink(args.infile, temp_link)
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74 args.infile = temp_link
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76 pool = multiprocessing.Pool(args.processors)
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77 for query in open(args.query):
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78 pool.apply_async(mp_helper, args=(query.strip(), args), callback=mp_callback)
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79 # mp_callback(mp_helper(query.strip(), args))
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80 pool.close()
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81 pool.join()
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83 out_handle = open(args.outfile, 'wb')
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84 for result_file, query in results:
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85 res_handle = open(result_file, 'rb')
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86 shutil.copyfileobj(res_handle, out_handle)
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87 res_handle.close()
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88 os.remove(result_file)
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89 out_handle.close()
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90
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91 os.remove(temp_link)
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92
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93
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94 def __main__():
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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95 """
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96 Multiprocessing obgrep search.
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97 """
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98 args = parse_command_line()
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99 obgrep(args)
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100
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101
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102 if __name__ == "__main__":
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103 __main__()