Mercurial > repos > bgruening > openbabel_filter

comparison multi_obgrep.py @ 13:ff2dd4b7d918 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
author bgruening
date Tue, 28 Jul 2020 08:40:01 -0400
parents 0d6e836460be
children 8ee975c49a3d
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12:340f8d63c1f4 13:ff2dd4b7d918
4 Output: Molecule file filtered with obgrep. 4 Output: Molecule file filtered with obgrep.
5 Copyright 2013, Bjoern Gruening and Xavier Lucas 5 Copyright 2013, Bjoern Gruening and Xavier Lucas
6 """ 6 """
7 import sys, os 7 import sys, os
8 import argparse 8 import argparse
9 import openbabel
10 openbabel.obErrorLog.StopLogging()
11 import pybel
12 import multiprocessing 9 import multiprocessing
13 import tempfile 10 import tempfile
14 import subprocess 11 import subprocess
15 import shutil 12 import shutil
16 import shlex 13 import shlex
17 14
15 from openbabel import openbabel, pybel
16 openbabel.obErrorLog.StopLogging()
18 def parse_command_line(): 17 def parse_command_line():
19 parser = argparse.ArgumentParser() 18 parser = argparse.ArgumentParser()
20 parser.add_argument('-i', '--infile', required=True, help='Molecule file.') 19 parser.add_argument('-i', '--infile', required=True, help='Molecule file.')
21 parser.add_argument('-q', '--query', required=True, help='Query file, containing different SMARTS in each line.') 20 parser.add_argument('-q', '--query', required=True, help='Query file, containing different SMARTS in each line.')
22 parser.add_argument('-o', '--outfile', required=True, help='Path to the output file.') 21 parser.add_argument('-o', '--outfile', required=True, help='Path to the output file.')