Mercurial > repos > bgruening > openbabel_genprop
diff ob_filter.py @ 13:417845394cdf draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
author | bgruening |
---|---|
date | Mon, 19 Oct 2020 14:46:54 +0000 |
parents | a72ae2711a97 |
children | 50eaae9df8d3 |
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--- a/ob_filter.py Tue Jul 28 08:34:42 2020 -0400 +++ b/ob_filter.py Mon Oct 19 14:46:54 2020 +0000 @@ -6,35 +6,32 @@ TODO: AND/OR conditions? """ -import sys, os import argparse +import json +import shlex +import subprocess +import sys + import cheminfolib -import json -import shlex, subprocess - 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', - help="A file with list of molecule names to extract. Every name is in one line.", - required=False, - ) + 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): @@ -53,6 +50,7 @@ outfile.write(mol) outfile.close() + def filter_new_compounds(args, filters): if args.iformat == args.oformat: @@ -70,10 +68,9 @@ 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) + # 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) + child = subprocess.Popen(args, stdout=subprocess.PIPE, stderr=subprocess.PIPE) stdout, stderr = child.communicate() return_code = child.returncode @@ -87,6 +84,7 @@ 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): @@ -95,16 +93,17 @@ 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. @@ -114,7 +113,7 @@ mol = next(pybel.readfile('sdf', args.input)) for key, elem in filters.items(): property = cheminfolib.ColumnNames.get(key, key) - if not property in mol.data: + 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 @@ -124,5 +123,5 @@ filter_new_compounds(args, filters) -if __name__ == "__main__" : +if __name__ == "__main__": __main__()