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annotate multi_obgrep.py @ 2:bf3b0107c0f4 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 78ac0521d7df684e96c1b9c1ba2a17b02e681608
author bgruening
date Sat, 20 May 2017 20:03:56 -0400
parents c9bee3591df9
children 354c048550f7
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c9bee3591df9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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1 #!/usr/bin/env python
c9bee3591df9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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2 """
c9bee3591df9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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3 Input: Molecules in SDF, SMILES ...
c9bee3591df9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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4 Output: Molecule file filtered with obgrep.
c9bee3591df9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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5 Copyright 2013, Bjoern Gruening and Xavier Lucas
c9bee3591df9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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6 """
c9bee3591df9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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7 import sys, os
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8 import argparse
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9 import openbabel
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10 openbabel.obErrorLog.StopLogging()
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11 import pybel
c9bee3591df9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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12 import multiprocessing
c9bee3591df9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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13 import tempfile
c9bee3591df9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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14 import subprocess
c9bee3591df9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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15 import shutil
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16 import shlex
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17
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18 def parse_command_line():
c9bee3591df9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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19 parser = argparse.ArgumentParser()
c9bee3591df9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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20 parser.add_argument('-i', '--infile', required=True, help='Molecule file.')
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21 parser.add_argument('-q', '--query', required=True, help='Query file, containing different SMARTS in each line.')
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22 parser.add_argument('-o', '--outfile', required=True, help='Path to the output file.')
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23 parser.add_argument("--iformat", help="Input format, like smi, sdf, inchi")
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24 parser.add_argument("--n-times", dest="n_times", type=int,
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25 default=0, help="Print a molecule only if the pattern occurs # times inside the molecule.")
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26 parser.add_argument('-p', '--processors', type=int, default=multiprocessing.cpu_count())
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27 parser.add_argument("--invert-matches", dest="invert_matches", action="store_true",
c9bee3591df9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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28 default=False, help="Invert the matching, print non-matching molecules.")
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29 parser.add_argument("--only-name", dest="only_name", action="store_true",
c9bee3591df9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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30 default=False, help="Only print the name of the molecules.")
c9bee3591df9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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31 parser.add_argument("--full-match", dest="full_match", action="store_true",
c9bee3591df9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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32 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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33 parser.add_argument("--number-of-matches", dest="number_of_matches", action="store_true",
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34 default=False, help="Print the number of matches.")
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35 return parser.parse_args()
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36
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37 results = list()
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38 def mp_callback(res):
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39 results.append(res)
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40
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41 def mp_helper( query, args ):
c9bee3591df9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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42 """
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43 Helper function for multiprocessing.
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44 That function is a wrapper around obgrep.
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45 """
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46
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47 cmd_list = []
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48 if args.invert_matches:
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49 cmd_list.append('-v')
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50 if args.only_name:
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51 cmd_list.append('-n')
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52 if args.full_match:
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53 cmd_list.append('-f')
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54 if args.number_of_matches:
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55 cmd_list.append('-c')
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56 if args.n_times:
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57 cmd_list.append('-t %s' % str(args.n_times))
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58
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59 tmp = tempfile.NamedTemporaryFile(delete=False)
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60 cmd = 'obgrep %s "%s" %s' % (' '.join(cmd_list), query, args.infile)
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61 child = subprocess.Popen(shlex.split(cmd),
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62 stdout=open(tmp.name, 'w+'), stderr=subprocess.PIPE)
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63
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64 stdout, stderr = child.communicate()
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65 return (tmp.name, query)
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66
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67
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68 def obgrep( args ):
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69
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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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75
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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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82
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83 out_handle = open( args.outfile, 'wb' )
c9bee3591df9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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84 for result_file, query in results:
c9bee3591df9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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85 res_handle = open(result_file,'rb')
c9bee3591df9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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86 shutil.copyfileobj( res_handle, out_handle )
c9bee3591df9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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87 res_handle.close()
c9bee3591df9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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88 os.remove( result_file )
c9bee3591df9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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89 out_handle.close()
c9bee3591df9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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90
c9bee3591df9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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91 os.remove( temp_link )
c9bee3591df9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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92
c9bee3591df9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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93 def __main__():
c9bee3591df9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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94 """
c9bee3591df9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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95 Multiprocessing obgrep search.
c9bee3591df9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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96 """
c9bee3591df9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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97 args = parse_command_line()
c9bee3591df9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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98 obgrep( args )
c9bee3591df9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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99
c9bee3591df9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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100 if __name__ == "__main__" :
c9bee3591df9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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101 __main__()