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view ob_filter.py @ 15:c5de6c19eb06 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
author | bgruening |
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date | Thu, 15 Aug 2024 11:00:46 +0000 |
parents | 12aca74f07d7 |
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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 argparse import json import shlex import subprocess import sys import cheminfolib from openbabel import pybel 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) parser.add_argument( "--list_of_names", required=False, help="A file with list of molecule names to extract. Every name is in one line.", ) 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.get(key, 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 filter_by_name(args): outfile = pybel.Outputfile(args.oformat, args.output, overwrite=True) for mol in pybel.readfile("sdf", args.input): for name in open(args.list_of_names): if mol.title.strip() == name.strip(): outfile.write(mol) outfile.close() def __main__(): """ Select compounds with certain properties from a small library """ args = parse_command_line() if args.filters == "__filter_by_name__": filter_by_name(args) return # 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.get(key, key) if property not 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__()