import argparse
import os
import sys
if sys.version_info.major < 3:
import ConfigParser
else:
import configparser as ConfigParser
from mrparse.mr_version import __version__
[docs]class FilePathAction(argparse.Action):
"""Class to handle paths to files or directories.
We cd into a work directory so relative paths to files don't work.
We set absolulte paths here.
"""
def __call__(self, parser, namespace, values, option_string=None):
if isinstance(values, str):
values = os.path.abspath(values)
setattr(namespace, self.dest, values)
[docs]def mrparse_argparse():
"""Parse MrParse command line arguments"""
# Read command line arguments
parser = argparse.ArgumentParser(description="MrParse Molecular Replacement Search Model analysis")
parser.add_argument('-hkl', '--hklin', action=FilePathAction, help='MTZ/CIF Crystal Data file')
parser.add_argument('--do_classify', action='store_true',
help='Run the SS/TM/CC classifiers - requires internet access.')
parser.add_argument('--pdb_dir', action=FilePathAction, help='Directory of PDB files')
parser.add_argument('--phmmer_dblvl', help='Redundancy level of PDB database used by Phmmer', default='95',
choices=['50', '70', '90', '95', '100'])
parser.add_argument('--run_serial', action='store_true', help='Run on a single processor')
parser.add_argument('-seq', '--seqin', action=FilePathAction, help='Sequence file')
parser.add_argument('--search_engine', help="Select search engine", default="phmmer",
choices=['phmmer', 'hhsearch'])
parser.add_argument('--tmhmm_exe', action=FilePathAction,
help="Location of TMHMM executable for transmembrane classification")
parser.add_argument('--deepcoil_exe', action=FilePathAction,
help="Location of Deepcoil executable for coiled-coil classification")
parser.add_argument('--hhsearch_exe', action=FilePathAction,
help="Location of hhsearch executable")
parser.add_argument('--hhsearch_db', help="Location of hhsearch database")
parser.add_argument('--ccp4cloud', action='store_true', help="specify running through CCP4Cloud")
parser.add_argument('-v', '--version', action='version', version='%(prog)s version: ' + __version__)
return parser
[docs]def parse_command_line():
"""Parse MrParse command line arguments"""
# Read config file, check for local config file for documentation
if os.path.isfile(os.path.join(os.path.dirname(os.path.abspath(__file__)), "..", "data", "mrparse.config")):
config_file = os.path.join(os.path.dirname(os.path.abspath(__file__)), "..", "data", "mrparse.config")
else:
config_file = os.path.join(os.environ["CCP4"], "share", "mrparse", "data", "mrparse.config")
defaults = {}
config = ConfigParser.SafeConfigParser()
config.read(config_file)
defaults.update(dict(config.items("Defaults")))
defaults.update(dict(config.items("Executables")))
defaults.update(dict(config.items("Databases")))
parser = mrparse_argparse()
parser.set_defaults(**defaults)
args = parser.parse_args()
# Add executables and databases to config file so that it only needs to be specified once
update_config = False
if args.tmhmm_exe != defaults['tmhmm_exe']:
config.set('Executables', 'tmhmm_exe', args.tmhmm_exe)
update_config = True
if args.deepcoil_exe != defaults['deepcoil_exe']:
config.set('Executables', 'deepcoil_exe', args.deepcoil_exe)
update_config = True
if args.hhsearch_exe != defaults['hhsearch_exe']:
config.set('Executables', 'hhsearch_exe', args.hhsearch_exe)
update_config = True
if args.hhsearch_db != defaults['hhsearch_db']:
config.set('Databases', 'hhsearch_db', args.hhsearch_db)
update_config = True
if update_config:
with open(config_file, 'w') as f:
config.write(f)
return args
