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annotate ob_filter.py @ 15:50eaae9df8d3 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 11:05:33 +0000
parents 417845394cdf
children
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df6d948e95ba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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1 #!/usr/bin/env python
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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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7 TODO: AND/OR conditions?
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8 """
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9 import argparse
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10 import json
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11 import shlex
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12 import subprocess
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13 import sys
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15 import cheminfolib
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16 from openbabel import pybel
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18 cheminfolib.pybel_stop_logging()
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21 def parse_command_line():
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22 parser = argparse.ArgumentParser()
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23 parser.add_argument("-i", "--input", help="Input file name")
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24 parser.add_argument("-iformat", help="Input file format")
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25 parser.add_argument("-oformat", default="smi", help="Output file format")
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26 parser.add_argument("-o", "--output", help="Output file name", required=True)
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27 parser.add_argument("--filters", help="Specify the filters to apply", required=True)
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28 parser.add_argument(
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29 "--list_of_names",
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30 required=False,
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31 help="A file with list of molecule names to extract. Every name is in one line.",
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32 )
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33 return parser.parse_args()
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36 def filter_precalculated_compounds(args, filters):
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37 outfile = pybel.Outputfile(args.oformat, args.output, overwrite=True)
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38 for mol in pybel.readfile("sdf", args.input):
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39 for key, elem in filters.items():
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40 # map the short description to the larger metadata names stored in the sdf file
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41 property = cheminfolib.ColumnNames.get(key, key)
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42 min = elem[0]
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43 max = elem[1]
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44 if float(mol.data[property]) >= float(min) and float(
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45 mol.data[property]
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46 ) <= 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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57 def filter_new_compounds(args, filters):
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58
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59 if args.iformat == args.oformat:
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60 # use the -ocopy option from openbabel to speed up the filtering, additionally no conversion is carried out
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61 # http://openbabel.org/docs/dev/FileFormats/Copy_raw_text.html#copy-raw-text
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62 cmd = "obabel -i%s %s -ocopy -O %s --filter" % (
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63 args.iformat,
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64 args.input,
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65 args.output,
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66 )
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67 else:
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68 cmd = "obabel -i%s %s -o%s -O %s --filter" % (
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69 args.iformat,
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70 args.input,
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71 args.oformat,
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72 args.output,
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73 )
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74 filter_cmd = ""
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75 # OBDescriptor stores a mapping from our desc shortcut to the OB name [0] and a long description [1]
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76 for key, elem in filters.items():
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77 ob_descriptor_name = cheminfolib.OBDescriptor[key][0]
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78 min = elem[0]
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79 max = elem[1]
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80 filter_cmd += " %s>=%s %s<=%s " % (
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81 ob_descriptor_name,
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82 min,
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83 ob_descriptor_name,
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84 max,
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85 )
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86
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87 args = shlex.split('%s "%s"' % (cmd, filter_cmd))
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88 # print '%s "%s"' % (cmd, filter_cmd)
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df6d948e95ba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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89 # calling openbabel with subprocess and pipe potential errors occuring in openbabel to stdout
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90 child = subprocess.Popen(args, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
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df6d948e95ba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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91
df6d948e95ba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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92 stdout, stderr = child.communicate()
df6d948e95ba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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93 return_code = child.returncode
df6d948e95ba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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94
df6d948e95ba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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95 if return_code:
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96 sys.stdout.write(stdout.decode("utf-8"))
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97 sys.stderr.write(stderr.decode("utf-8"))
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df6d948e95ba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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98 sys.stderr.write("Return error code %i from command:\n" % return_code)
df6d948e95ba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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99 sys.stderr.write("%s\n" % cmd)
df6d948e95ba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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100 else:
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101 sys.stdout.write(stdout.decode("utf-8"))
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102 sys.stdout.write(stderr.decode("utf-8"))
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103
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104
10
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105 def filter_by_name(args):
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106 outfile = pybel.Outputfile(args.oformat, args.output, overwrite=True)
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107 for mol in pybel.readfile("sdf", args.input):
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108 for name in open(args.list_of_names):
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109 if mol.title.strip() == name.strip():
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110 outfile.write(mol)
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111 outfile.close()
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112
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113
0
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114 def __main__():
df6d948e95ba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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115 """
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116 Select compounds with certain properties from a small library
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117 """
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118 args = parse_command_line()
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119
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120 if args.filters == "__filter_by_name__":
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121 filter_by_name(args)
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122 return
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123
0
df6d948e95ba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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124 # Its a small trick to get the parameters in an easy way from the xml file.
df6d948e95ba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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125 # To keep it readable in the xml file, many white-spaces are included in that string it needs to be removed.
df6d948e95ba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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126 # Also the last loop creates a ',{' that is not an valid jason expression.
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127 filters = json.loads((args.filters).replace(" ", "").replace(",}", "}"))
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128 if args.iformat == "sdf":
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129 # Check if the sdf file contains all of the required metadata to invoke the precalculation filtering
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130 mol = next(pybel.readfile("sdf", args.input))
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df6d948e95ba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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131 for key, elem in filters.items():
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132 property = cheminfolib.ColumnNames.get(key, key)
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133 if property not in mol.data:
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134 break
df6d948e95ba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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135 else:
df6d948e95ba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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136 # if the for loop finishes in a normal way, we should habe all properties at least in the first molecule
df6d948e95ba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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137 # assume it is the same for all other molecules and start the precalculated filtering
df6d948e95ba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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138 filter_precalculated_compounds(args, filters)
df6d948e95ba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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139 return True
df6d948e95ba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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140 filter_new_compounds(args, filters)
df6d948e95ba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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141
df6d948e95ba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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142
13
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143 if __name__ == "__main__":
0
df6d948e95ba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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144 __main__()