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annotate ob_filter.py @ 1:f81e9050185a draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 63d8775d73dd16e3ee8836ea8c06c81801e87c71
author bgruening
date Mon, 28 Nov 2016 02:08:51 -0500
parents a5c2ba5793c8
children
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a5c2ba5793c8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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1 #!/usr/bin/env python
a5c2ba5793c8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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2 """
a5c2ba5793c8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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3 Input: set of molecules with pre-calculated physico-chemical properties
a5c2ba5793c8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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4 Output: set of molecules that pass all the filters
a5c2ba5793c8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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5 Copyright 2012, Bjoern Gruening and Xavier Lucas
a5c2ba5793c8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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6
a5c2ba5793c8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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7 TODO: AND/OR conditions?
a5c2ba5793c8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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8 """
a5c2ba5793c8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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9 import sys, os
a5c2ba5793c8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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10 import argparse
a5c2ba5793c8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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11 import cheminfolib
a5c2ba5793c8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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12 import json
a5c2ba5793c8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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13 import pybel
a5c2ba5793c8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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14 import shlex, subprocess
a5c2ba5793c8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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15
a5c2ba5793c8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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16 cheminfolib.pybel_stop_logging()
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17
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18 def parse_command_line():
a5c2ba5793c8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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19 parser = argparse.ArgumentParser()
a5c2ba5793c8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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20 parser.add_argument('-i', '--input', help='Input file name')
a5c2ba5793c8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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21 parser.add_argument('-iformat', help='Input file format')
a5c2ba5793c8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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22 parser.add_argument('-oformat',
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23 default='smi',
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24 help='Output file format')
a5c2ba5793c8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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25 parser.add_argument('-o', '--output',
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26 help='Output file name',
a5c2ba5793c8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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27 required=True)
a5c2ba5793c8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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28 parser.add_argument('--filters',
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29 help="Specify the filters to apply",
a5c2ba5793c8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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30 required=True,
a5c2ba5793c8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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31 )
a5c2ba5793c8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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32 return parser.parse_args()
a5c2ba5793c8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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33
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34 def filter_precalculated_compounds(args, filters):
a5c2ba5793c8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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35 outfile = pybel.Outputfile(args.oformat, args.output, overwrite=True)
a5c2ba5793c8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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36 for mol in pybel.readfile('sdf', args.input):
a5c2ba5793c8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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37 for key, elem in filters.items():
a5c2ba5793c8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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38 # map the short description to the larger metadata names stored in the sdf file
a5c2ba5793c8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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39 property = cheminfolib.ColumnNames[key]
a5c2ba5793c8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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40 min = elem[0]
a5c2ba5793c8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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41 max = elem[1]
a5c2ba5793c8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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42 if float(mol.data[property]) >= float(min) and float(mol.data[property]) <= float(max):
a5c2ba5793c8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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43 pass
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44 else:
a5c2ba5793c8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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45 # leave the filter loop, because one filter constrained are not satisfied
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46 break
a5c2ba5793c8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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47 else:
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48 # if the filter loop terminates in a normal way (no break) all filter rules are satisfied, so save the compound
a5c2ba5793c8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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49 outfile.write(mol)
a5c2ba5793c8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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50 outfile.close()
a5c2ba5793c8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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51
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52 def filter_new_compounds(args, filters):
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53
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54 if args.iformat == args.oformat:
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55 # use the -ocopy option from openbabel to speed up the filtering, additionally no conversion is carried out
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56 # http://openbabel.org/docs/dev/FileFormats/Copy_raw_text.html#copy-raw-text
a5c2ba5793c8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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57 cmd = 'obabel -i%s %s -ocopy -O %s --filter' % (args.iformat, args.input, args.output)
a5c2ba5793c8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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58 else:
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59 cmd = 'obabel -i%s %s -o%s -O %s --filter' % (args.iformat, args.input, args.oformat, args.output)
a5c2ba5793c8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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60 filter_cmd = ''
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61 # OBDescriptor stores a mapping from our desc shortcut to the OB name [0] and a long description [1]
a5c2ba5793c8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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62 for key, elem in filters.items():
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63 ob_descriptor_name = cheminfolib.OBDescriptor[key][0]
a5c2ba5793c8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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64 min = elem[0]
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65 max = elem[1]
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66 filter_cmd += ' %s>=%s %s<=%s ' % (ob_descriptor_name, min, ob_descriptor_name, max)
a5c2ba5793c8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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67
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68 args = shlex.split('%s "%s"' % (cmd, filter_cmd))
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69 #print '%s "%s"' % (cmd, filter_cmd)
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70 # calling openbabel with subprocess and pipe potential errors occuring in openbabel to stdout
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71 child = subprocess.Popen(args,
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72 stdout=subprocess.PIPE, stderr=subprocess.PIPE)
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73
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74 stdout, stderr = child.communicate()
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75 return_code = child.returncode
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76
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77 if return_code:
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78 sys.stdout.write(stdout)
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79 sys.stderr.write(stderr)
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80 sys.stderr.write("Return error code %i from command:\n" % return_code)
a5c2ba5793c8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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81 sys.stderr.write("%s\n" % cmd)
a5c2ba5793c8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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82 else:
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83 sys.stdout.write(stdout)
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84 sys.stdout.write(stderr)
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85
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86
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87 def __main__():
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88 """
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89 Select compounds with certain properties from a small library
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90 """
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91 args = parse_command_line()
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92 # Its a small trick to get the parameters in an easy way from the xml file.
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93 # 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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94 # Also the last loop creates a ',{' that is not an valid jason expression.
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95 filters = json.loads((args.filters).replace(' ', '').replace(',}', '}'))
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96 if args.iformat == 'sdf':
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97 # Check if the sdf file contains all of the required metadata to invoke the precalculation filtering
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98 mol = pybel.readfile('sdf', args.input).next()
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99 for key, elem in filters.items():
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100 property = cheminfolib.ColumnNames[key]
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101 if not property in mol.data:
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102 break
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103 else:
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104 # if the for loop finishes in a normal way, we should habe all properties at least in the first molecule
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105 # assume it is the same for all other molecules and start the precalculated filtering
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106 filter_precalculated_compounds(args, filters)
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107 return True
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108 filter_new_compounds(args, filters)
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109
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110
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111 if __name__ == "__main__" :
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112 __main__()