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annotate ob_filter.py @ 10:3e47fe480f11 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 6c84abdd07f292048bf2194073e2e938e94158c4"
author bgruening
date Wed, 25 Mar 2020 20:33:49 +0000 (2020-03-25)
parents ca5c58399577
children 75e06b179e6b
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1 #!/usr/bin/env python
3286789c2e4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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2 """
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3 Input: set of molecules with pre-calculated physico-chemical properties
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4 Output: set of molecules that pass all the filters
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5 Copyright 2012, Bjoern Gruening and Xavier Lucas
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6
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7 TODO: AND/OR conditions?
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8 """
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9 import sys, os
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10 import argparse
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11 import cheminfolib
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12 import json
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13 import pybel
3286789c2e4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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14 import shlex, subprocess
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15
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16 cheminfolib.pybel_stop_logging()
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17
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18 def parse_command_line():
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19 parser = argparse.ArgumentParser()
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20 parser.add_argument('-i', '--input', help='Input file name')
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21 parser.add_argument('-iformat', help='Input file format')
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22 parser.add_argument('-oformat',
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23 default='smi',
3286789c2e4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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24 help='Output file format')
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25 parser.add_argument('-o', '--output',
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26 help='Output file name',
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27 required=True)
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28 parser.add_argument('--filters',
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29 help="Specify the filters to apply",
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30 required=True,
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31 )
10
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32 parser.add_argument('--list_of_names',
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33 help="A file with list of molecule names to extract. Every name is in one line.",
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34 required=False,
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35 )
0
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36 return parser.parse_args()
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37
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38 def filter_precalculated_compounds(args, filters):
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39 outfile = pybel.Outputfile(args.oformat, args.output, overwrite=True)
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40 for mol in pybel.readfile('sdf', args.input):
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41 for key, elem in filters.items():
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42 # map the short description to the larger metadata names stored in the sdf file
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43 property = cheminfolib.ColumnNames[key]
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44 min = elem[0]
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45 max = elem[1]
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46 if float(mol.data[property]) >= float(min) and float(mol.data[property]) <= float(max):
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47 pass
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48 else:
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49 # leave the filter loop, because one filter constrained are not satisfied
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50 break
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51 else:
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52 # if the filter loop terminates in a normal way (no break) all filter rules are satisfied, so save the compound
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53 outfile.write(mol)
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54 outfile.close()
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55
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56 def filter_new_compounds(args, filters):
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57
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58 if args.iformat == args.oformat:
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59 # use the -ocopy option from openbabel to speed up the filtering, additionally no conversion is carried out
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60 # http://openbabel.org/docs/dev/FileFormats/Copy_raw_text.html#copy-raw-text
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61 cmd = 'obabel -i%s %s -ocopy -O %s --filter' % (args.iformat, args.input, args.output)
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62 else:
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63 cmd = 'obabel -i%s %s -o%s -O %s --filter' % (args.iformat, args.input, args.oformat, args.output)
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64 filter_cmd = ''
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65 # OBDescriptor stores a mapping from our desc shortcut to the OB name [0] and a long description [1]
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66 for key, elem in filters.items():
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67 ob_descriptor_name = cheminfolib.OBDescriptor[key][0]
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68 min = elem[0]
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69 max = elem[1]
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70 filter_cmd += ' %s>=%s %s<=%s ' % (ob_descriptor_name, min, ob_descriptor_name, max)
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71
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72 args = shlex.split('%s "%s"' % (cmd, filter_cmd))
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73 #print '%s "%s"' % (cmd, filter_cmd)
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74 # calling openbabel with subprocess and pipe potential errors occuring in openbabel to stdout
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75 child = subprocess.Popen(args,
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76 stdout=subprocess.PIPE, stderr=subprocess.PIPE)
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77
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78 stdout, stderr = child.communicate()
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79 return_code = child.returncode
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80
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81 if return_code:
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82 sys.stdout.write(stdout.decode('utf-8'))
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83 sys.stderr.write(stderr.decode('utf-8'))
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84 sys.stderr.write("Return error code %i from command:\n" % return_code)
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85 sys.stderr.write("%s\n" % cmd)
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86 else:
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87 sys.stdout.write(stdout.decode('utf-8'))
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88 sys.stdout.write(stderr.decode('utf-8'))
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89
10
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90 def filter_by_name(args):
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91 outfile = pybel.Outputfile(args.oformat, args.output, overwrite=True)
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92 for mol in pybel.readfile('sdf', args.input):
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93 for name in open(args.list_of_names):
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94 if mol.title.strip() == name.strip():
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95 outfile.write(mol)
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96 outfile.close()
0
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97
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98 def __main__():
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99 """
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100 Select compounds with certain properties from a small library
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101 """
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102 args = parse_command_line()
10
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103
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104 if args.filters == '__filter_by_name__':
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105 filter_by_name(args)
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106 return
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107
0
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108 # Its a small trick to get the parameters in an easy way from the xml file.
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109 # To keep it readable in the xml file, many white-spaces are included in that string it needs to be removed.
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110 # Also the last loop creates a ',{' that is not an valid jason expression.
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111 filters = json.loads((args.filters).replace(' ', '').replace(',}', '}'))
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112 if args.iformat == 'sdf':
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113 # Check if the sdf file contains all of the required metadata to invoke the precalculation filtering
2
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114 mol = next(pybel.readfile('sdf', args.input))
0
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115 for key, elem in filters.items():
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116 property = cheminfolib.ColumnNames[key]
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117 if not property in mol.data:
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118 break
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119 else:
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120 # if the for loop finishes in a normal way, we should habe all properties at least in the first molecule
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121 # assume it is the same for all other molecules and start the precalculated filtering
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122 filter_precalculated_compounds(args, filters)
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123 return True
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124 filter_new_compounds(args, filters)
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125
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126
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127 if __name__ == "__main__" :
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128 __main__()