def main():
"""The main work of processing the command-line arguments and then
converting the Bio-PEPA file into LaTeX
"""
description = "Translates Bio-PEPA model files to LaTeX"
file_help = "A model file to translate to LaTeX"
parser = utils.argparser_withfiles(description, file_help, True)
utils.add_output_file_arg(parser)
arguments = parser.parse_args()
for biopepa_file in arguments.filenames:
latexify_file(biopepa_file, arguments)
def run():
"""Perform the banalities of command-line argument processing
and then do the actual work on each argument file
"""
description = "Convert SBML models into facile model files" ""
parser = argparse.ArgumentParser(description=description)
# Might want to make the type of this 'FileType('r')'
parser.add_argument("filenames", metavar="F", nargs="+", help="an SBML file to translate to facile")
utils.add_output_file_arg(parser)
arguments = parser.parse_args()
for filename in arguments.filenames:
convert_file(filename, arguments)
def main():
"""A simple main function to parse in the arguments as
Bio-PEPA model files"""
description = "Flattens a Bio-PEPA model to remove compartments"
parser = argparse.ArgumentParser(add_help=True,
description=description)
# Might want to make the type of this 'FileType('r')'
parser.add_argument('filenames', metavar='F', nargs='+',
help="A Bio-PEPA model file to flatten")
utils.add_output_file_arg(parser)
arguments = parser.parse_args()
for filename in arguments.filenames:
process_file(filename, arguments)
def run():
""" Command-line argument processing and then real work.
"""
description = "Convert SBML models into Bio-PEPA model files"
parser = argparse.ArgumentParser(description=description)
# Might want to make the type of this 'FileType('r')'
parser.add_argument('filenames', metavar='F', nargs='+',
help="an SBML file to translate to Bio-PEPA")
utils.add_output_file_arg(parser)
arguments = parser.parse_args()
for filename in arguments.filenames:
translate_file(filename, arguments)
def main():
"""A simple main function to parse in the arguments as
Bio-PEPA model files"""
description = "Translates Bio-PEPA model files to SBML"
parser = argparse.ArgumentParser(add_help=True,
description=description)
# Might want to make the type of this 'FileType('r')'
parser.add_argument('filenames', metavar='F', nargs='+',
help="A Bio-PEPA model file to translate")
utils.add_output_file_arg(parser)
arguments = parser.parse_args()
for filename in arguments.filenames:
convert_file(filename, arguments)
def create_arguments_parser():
"""
Create an arguments parser to be used as a basis for
all argument parsers for modifying timeseries scripts.
"""
parser = argparse.ArgumentParser(add_help=False)
# Might want to make the type of this 'FileType('r')'
parser.add_argument('filenames', metavar='F', nargs='+',
help="the input files, should be exactly two")
parser.add_argument('--column', action=utils.ListArgumentAction,
help="Specify a column to be in the output")
parser.add_argument('--mcolumn', action=utils.ListArgumentAction,
help="Specify a column not to be in the output")
utils.add_output_file_arg(parser)
return parser
def main():
"""A simple main function to parse in the arguments
as facile model file
"""
description = "Translate facile model file(s) into sbml"
parent_arg_parser = static_analyser_sbml.create_arguments_parser()
parser = argparse.ArgumentParser(description=description,
parents=[parent_arg_parser]
)
# Might want to make the type of this 'FileType('r')'
parser.add_argument('filenames', metavar='F', nargs='+',
help="A facile model file to translate")
parser.add_argument('--add-modifiers', action='store_true',
help="Species mentioned in kinetic law added as modifiers")
parser.add_argument('--copasi-spec-ref-workaround', action='store_true',
help="Works around a copasi bug by not setting a constant attribute")
parser.add_argument('--no-static-analysis', action='store_true',
help="Suppresses post-translation static analysis")
utils.add_output_file_arg(parser)
arguments = parser.parse_args()
for filename in arguments.filenames:
translate_file(filename, arguments)