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annotate subsearch.py @ 14:985ab0acd514 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 11:05:06 +0000
parents 2912ebf12ef2
children
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b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
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1 #!/usr/bin/env python
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
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2 """
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3 Input: Molecules in SDF, SMILES ...
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4 Output: Moleculs filtered with specified substructures.
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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 shutil
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11 import subprocess
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12 import sys
2912ebf12ef2 "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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14
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15 from openbabel import openbabel, pybel
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17 openbabel.obErrorLog.StopLogging()
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20 def parse_command_line():
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21 parser = argparse.ArgumentParser()
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22 parser.add_argument("-i", "--infile", required=True, help="Molecule file.")
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23 parser.add_argument("--iformat", help="Input format.")
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24 parser.add_argument(
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25 "--fastsearch-index",
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26 dest="fastsearch_index",
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27 required=True,
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28 help="Path to the openbabel fastsearch index.",
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29 )
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30 parser.add_argument(
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31 "-o", "--outfile", required=True, help="Path to the output file."
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32 )
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33 parser.add_argument("--oformat", default="smi", help="Output file format")
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34 parser.add_argument(
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35 "--max-candidates",
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36 dest="max_candidates",
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37 type=int,
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38 default=4000,
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39 help="The maximum number of candidates.",
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40 )
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41 parser.add_argument(
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42 "-p", "--processors", type=int, default=multiprocessing.cpu_count()
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43 )
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44 return parser.parse_args()
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47 results = list()
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50 def mp_callback(res):
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51 results.append(res)
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54 def mp_helper(query, args):
0
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55 """
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56 Helper function for multiprocessing.
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57 That function is a wrapper around the following command:
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58 obabel file.fs -s"smarts" -Ooutfile.smi -al 999999999
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59 """
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61 if args.oformat == "names":
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62 opts = "-osmi -xt"
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63 else:
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64 opts = "-o%s" % args.oformat
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66 tmp = tempfile.NamedTemporaryFile(delete=False)
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67 cmd = "obabel -ifs %s -O %s %s -s%s -al %s" % (
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68 args.fastsearch_index,
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69 tmp.name,
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70 opts,
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71 query,
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72 args.max_candidates,
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73 )
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75 child = subprocess.Popen(
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76 cmd.split(), stdout=subprocess.PIPE, stderr=subprocess.PIPE
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77 )
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79 stdout, stderr = child.communicate()
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80 return_code = child.returncode
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82 if return_code:
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83 sys.stdout.write(stdout)
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84 sys.stderr.write(stderr)
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85 sys.stderr.write("Return error code %i from command:\n" % return_code)
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86 sys.stderr.write("%s\n" % cmd)
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87 else:
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88 sys.stdout.write(stdout)
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89 sys.stdout.write(stderr)
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90 return (tmp.name, query)
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91
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92
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93 def get_smiles_or_smarts(args):
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94 """
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95 Wrapper to retrieve a striped SMILES or SMARTS string from different input formats.
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96 """
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97 if args.iformat in ["smi", "text", "tabular"]:
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98 with open(args.infile) as text_file:
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99 for line in text_file:
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100 yield line.split("\t")[0].strip()
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101 else:
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102 # inchi or sdf files
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103 for mol in pybel.readfile(args.iformat, args.infile):
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104 yield mol.write("smiles").split("\t")[0]
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105
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106
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107 def substructure_search(args):
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108 pool = multiprocessing.Pool(args.processors)
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109 for query in get_smiles_or_smarts(args):
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110 pool.apply_async(mp_helper, args=(query, args), callback=mp_callback)
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111 # mp_callback(mp_helper(query, args))
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112 pool.close()
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113 pool.join()
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114
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115 if args.oformat == "names":
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116 out_handle = open(args.outfile, "w")
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117 for result_file, query in results:
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118 with open(result_file) as res_handle:
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119 for line in res_handle:
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120 out_handle.write("%s\t%s\n" % (line.strip(), query))
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121 os.remove(result_file)
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122 out_handle.close()
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123 else:
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124 out_handle = open(args.outfile, "wb")
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125 for result_file, query in results:
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126 res_handle = open(result_file, "rb")
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127 shutil.copyfileobj(res_handle, out_handle)
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128 res_handle.close()
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129 os.remove(result_file)
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130 out_handle.close()
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131
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132
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133 def __main__():
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134 """
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135 Multiprocessing Open Babel Substructure Search.
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136 """
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137 args = parse_command_line()
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138 substructure_search(args)
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139
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140
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141 if __name__ == "__main__":
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142 __main__()