Mercurial > repos > bgruening > openbabel_multi_obgrep
view ob_filter.py @ 4:e1e344bd8a84 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c84729ec58f7f52d594066158afed175208d3d66
author | bgruening |
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date | Wed, 24 May 2017 10:01:44 -0400 |
parents | a7d741129d47 |
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#!/usr/bin/env python """ Input: set of molecules with pre-calculated physico-chemical properties Output: set of molecules that pass all the filters Copyright 2012, Bjoern Gruening and Xavier Lucas TODO: AND/OR conditions? """ import sys, os import argparse import cheminfolib import json import pybel import shlex, subprocess cheminfolib.pybel_stop_logging() def parse_command_line(): parser = argparse.ArgumentParser() parser.add_argument('-i', '--input', help='Input file name') parser.add_argument('-iformat', help='Input file format') parser.add_argument('-oformat', default='smi', help='Output file format') parser.add_argument('-o', '--output', help='Output file name', required=True) parser.add_argument('--filters', help="Specify the filters to apply", required=True, ) return parser.parse_args() def filter_precalculated_compounds(args, filters): outfile = pybel.Outputfile(args.oformat, args.output, overwrite=True) for mol in pybel.readfile('sdf', args.input): for key, elem in filters.items(): # map the short description to the larger metadata names stored in the sdf file property = cheminfolib.ColumnNames[key] min = elem[0] max = elem[1] if float(mol.data[property]) >= float(min) and float(mol.data[property]) <= float(max): pass else: # leave the filter loop, because one filter constrained are not satisfied break else: # if the filter loop terminates in a normal way (no break) all filter rules are satisfied, so save the compound outfile.write(mol) outfile.close() def filter_new_compounds(args, filters): if args.iformat == args.oformat: # use the -ocopy option from openbabel to speed up the filtering, additionally no conversion is carried out # http://openbabel.org/docs/dev/FileFormats/Copy_raw_text.html#copy-raw-text cmd = 'obabel -i%s %s -ocopy -O %s --filter' % (args.iformat, args.input, args.output) else: cmd = 'obabel -i%s %s -o%s -O %s --filter' % (args.iformat, args.input, args.oformat, args.output) filter_cmd = '' # OBDescriptor stores a mapping from our desc shortcut to the OB name [0] and a long description [1] for key, elem in filters.items(): ob_descriptor_name = cheminfolib.OBDescriptor[key][0] min = elem[0] max = elem[1] filter_cmd += ' %s>=%s %s<=%s ' % (ob_descriptor_name, min, ob_descriptor_name, max) args = shlex.split('%s "%s"' % (cmd, filter_cmd)) #print '%s "%s"' % (cmd, filter_cmd) # calling openbabel with subprocess and pipe potential errors occuring in openbabel to stdout child = subprocess.Popen(args, stdout=subprocess.PIPE, stderr=subprocess.PIPE) stdout, stderr = child.communicate() return_code = child.returncode if return_code: sys.stdout.write(stdout.decode('utf-8')) sys.stderr.write(stderr.decode('utf-8')) sys.stderr.write("Return error code %i from command:\n" % return_code) sys.stderr.write("%s\n" % cmd) else: sys.stdout.write(stdout.decode('utf-8')) sys.stdout.write(stderr.decode('utf-8')) def __main__(): """ Select compounds with certain properties from a small library """ args = parse_command_line() # Its a small trick to get the parameters in an easy way from the xml file. # To keep it readable in the xml file, many white-spaces are included in that string it needs to be removed. # Also the last loop creates a ',{' that is not an valid jason expression. filters = json.loads((args.filters).replace(' ', '').replace(',}', '}')) if args.iformat == 'sdf': # Check if the sdf file contains all of the required metadata to invoke the precalculation filtering mol = next(pybel.readfile('sdf', args.input)) for key, elem in filters.items(): property = cheminfolib.ColumnNames[key] if not property in mol.data: break else: # if the for loop finishes in a normal way, we should habe all properties at least in the first molecule # assume it is the same for all other molecules and start the precalculated filtering filter_precalculated_compounds(args, filters) return True filter_new_compounds(args, filters) if __name__ == "__main__" : __main__()