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annotate multi_obgrep.py @ 15:f3099132512d draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
author bgruening
date Thu, 15 Aug 2024 10:54:17 +0000
parents d44de092fef3
children
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112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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1 #!/usr/bin/env python
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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2 """
112341e4fc94 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 ...
112341e4fc94 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.
112341e4fc94 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
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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6 """
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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7 import argparse
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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8 import multiprocessing
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9 import os
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112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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10 import shlex
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11 import shutil
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12 import subprocess
d44de092fef3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
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13 import tempfile
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112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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14
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15
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112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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16 def parse_command_line():
112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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17 parser = argparse.ArgumentParser()
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18 parser.add_argument("-i", "--infile", required=True, help="Molecule file.")
f3099132512d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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19 parser.add_argument(
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20 "-q",
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21 "--query",
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22 required=True,
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23 help="Query file, containing different SMARTS in each line.",
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24 )
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25 parser.add_argument(
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26 "-o", "--outfile", required=True, help="Path to the output file."
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27 )
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112341e4fc94 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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28 parser.add_argument("--iformat", help="Input format, like smi, sdf, inchi")
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29 parser.add_argument(
f3099132512d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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30 "--n-times",
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31 dest="n_times",
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32 type=int,
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33 default=0,
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34 help="Print a molecule only if the pattern occurs # times inside the molecule.",
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35 )
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36 parser.add_argument(
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37 "-p", "--processors", type=int, default=multiprocessing.cpu_count()
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38 )
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39 parser.add_argument(
f3099132512d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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40 "--invert-matches",
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41 dest="invert_matches",
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42 action="store_true",
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43 default=False,
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44 help="Invert the matching, print non-matching molecules.",
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45 )
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46 parser.add_argument(
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47 "--only-name",
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48 dest="only_name",
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49 action="store_true",
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50 default=False,
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51 help="Only print the name of the molecules.",
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52 )
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53 parser.add_argument(
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54 "--full-match",
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55 dest="full_match",
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56 action="store_true",
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57 default=False,
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58 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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59 )
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60 parser.add_argument(
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61 "--number-of-matches",
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62 dest="number_of_matches",
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63 action="store_true",
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64 default=False,
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65 help="Print the number of matches.",
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66 )
0
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67 return parser.parse_args()
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68
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69
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70 results = list()
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72
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73 def mp_callback(res):
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74 results.append(res)
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75
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77 def mp_helper(query, args):
0
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78 """
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79 Helper function for multiprocessing.
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80 That function is a wrapper around obgrep.
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81 """
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82
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83 cmd_list = []
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84 if args.invert_matches:
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85 cmd_list.append("-v")
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86 if args.only_name:
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87 cmd_list.append("-n")
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88 if args.full_match:
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89 cmd_list.append("-f")
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90 if args.number_of_matches:
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91 cmd_list.append("-c")
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92 if args.n_times:
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93 cmd_list.append("-t %s" % str(args.n_times))
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94
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95 tmp = tempfile.NamedTemporaryFile(delete=False)
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96 cmd = 'obgrep %s "%s" %s' % (" ".join(cmd_list), query, args.infile)
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97 child = subprocess.Popen(
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98 shlex.split(cmd), stdout=open(tmp.name, "w+"), stderr=subprocess.PIPE
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99 )
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100
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101 stdout, stderr = child.communicate()
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102 return (tmp.name, query)
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103
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104
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105 def obgrep(args):
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106 temp_file = tempfile.NamedTemporaryFile()
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107 temp_link = "%s.%s" % (temp_file.name, args.iformat)
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108 temp_file.close()
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109 os.symlink(args.infile, temp_link)
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110 args.infile = temp_link
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111
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112 pool = multiprocessing.Pool(args.processors)
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113 for query in open(args.query):
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114 pool.apply_async(mp_helper, args=(query.strip(), args), callback=mp_callback)
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115 # mp_callback(mp_helper(query.strip(), args))
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116 pool.close()
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117 pool.join()
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118
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119 out_handle = open(args.outfile, "wb")
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120 for result_file, query in results:
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121 res_handle = open(result_file, "rb")
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122 shutil.copyfileobj(res_handle, out_handle)
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123 res_handle.close()
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124 os.remove(result_file)
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125 out_handle.close()
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126
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127 os.remove(temp_link)
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128
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129
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130 def __main__():
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131 """
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132 Multiprocessing obgrep search.
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133 """
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134 args = parse_command_line()
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135 obgrep(args)
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136
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137
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138 if __name__ == "__main__":
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139 __main__()