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annotate subsearch.py @ 14:6e4b7e0c61a6 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 327c29cc43f56d7067ab9fa51323ea31951db98b"
author bgruening
date Tue, 10 Nov 2020 20:36:42 +0000
parents f697d9601273
children 7b6fd1c273cd
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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: 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
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13 import tempfile
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14
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43167f164076 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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15 from openbabel import openbabel, pybel
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16 openbabel.obErrorLog.StopLogging()
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19 def parse_command_line():
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20 parser = argparse.ArgumentParser()
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21 parser.add_argument('-i', '--infile', required=True, help='Molecule file.')
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22 parser.add_argument('--iformat', help='Input format.')
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23 parser.add_argument('--fastsearch-index', dest="fastsearch_index", required=True,
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24 help='Path to the openbabel fastsearch index.')
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25 parser.add_argument('-o', '--outfile', required=True, help='Path to the output file.')
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26 parser.add_argument('--oformat', default='smi', help='Output file format')
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27 parser.add_argument("--max-candidates", dest="max_candidates", type=int, default=4000,
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28 help="The maximum number of candidates.")
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29 parser.add_argument('-p', '--processors', type=int,
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30 default=multiprocessing.cpu_count())
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31 return parser.parse_args()
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34 results = list()
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37 def mp_callback(res):
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38 results.append(res)
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41 def mp_helper(query, args):
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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 the following command:
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45 obabel file.fs -s"smarts" -Ooutfile.smi -al 999999999
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46 """
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48 if args.oformat == 'names':
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49 opts = '-osmi -xt'
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50 else:
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51 opts = '-o%s' % args.oformat
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52
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53 tmp = tempfile.NamedTemporaryFile(delete=False)
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54 cmd = 'obabel -ifs %s -O %s %s -s%s -al %s' % (args.fastsearch_index, tmp.name, opts, query, args.max_candidates)
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56 child = subprocess.Popen(cmd.split(), stdout=subprocess.PIPE, stderr=subprocess.PIPE)
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58 stdout, stderr = child.communicate()
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59 return_code = child.returncode
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61 if return_code:
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62 sys.stdout.write(stdout)
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63 sys.stderr.write(stderr)
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64 sys.stderr.write("Return error code %i from command:\n" % return_code)
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65 sys.stderr.write("%s\n" % cmd)
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66 else:
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67 sys.stdout.write(stdout)
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68 sys.stdout.write(stderr)
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69 return (tmp.name, query)
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72 def get_smiles_or_smarts(args):
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73 """
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74 Wrapper to retrieve a striped SMILES or SMARTS string from different input formats.
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75 """
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76 if args.iformat in ['smi', 'text', 'tabular']:
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77 with open(args.infile) as text_file:
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78 for line in text_file:
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79 yield line.split('\t')[0].strip()
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80 else:
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81 # inchi or sdf files
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82 for mol in pybel.readfile(args.iformat, args.infile):
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83 yield mol.write('smiles').split('\t')[0]
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86 def substructure_search(args):
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87 pool = multiprocessing.Pool(args.processors)
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88 for query in get_smiles_or_smarts(args):
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89 pool.apply_async(mp_helper, args=(query, args), callback=mp_callback)
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90 # mp_callback(mp_helper(query, args))
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91 pool.close()
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92 pool.join()
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93
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94 if args.oformat == 'names':
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95 out_handle = open(args.outfile, 'w')
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96 for result_file, query in results:
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97 with open(result_file) as res_handle:
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98 for line in res_handle:
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99 out_handle.write('%s\t%s\n' % (line.strip(), query))
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100 os.remove(result_file)
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101 out_handle.close()
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102 else:
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103 out_handle = open(args.outfile, 'wb')
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104 for result_file, query in results:
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105 res_handle = open(result_file, 'rb')
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106 shutil.copyfileobj(res_handle, out_handle)
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107 res_handle.close()
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108 os.remove(result_file)
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109 out_handle.close()
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110
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111
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112 def __main__():
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113 """
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114 Multiprocessing Open Babel Substructure Search.
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115 """
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116 args = parse_command_line()
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117 substructure_search(args)
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118
0
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119
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120 if __name__ == "__main__":
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121 __main__()