def main():
parser = defineConsole()
namespace = parser.parse_args()
options = checkInput(namespace)
returnArray = ls2b.analyzeFile(options['inputFile'],
options['conventionFile'],
options['useId'],
options['namingConventions'],
options['outputFile'],
speciesEquivalence=options['userStructure'],
atomize=options['atomize'],
bioGrid=False,
pathwaycommons=options['pathwaycommons'],
ignore=options['ignore'],
noConversion=options['noConversion'])
if namespace.bionetgen_analysis and returnArray:
ls2b.postAnalyzeFile(options['outputFile'],
namespace.bionetgen_analysis,
returnArray.database)
if namespace.annotation and returnArray:
with open(options['outputFile'] + '.yml', 'w') as f:
f.write(yaml.dump(returnArray.annotation,
default_flow_style=False))
def main():
parser = defineConsole()
namespace = parser.parse_args()
options = checkInput(namespace)
returnArray = ls2b.analyzeFile(options['inputFile'], options['conventionFile'], options['useId'], options['namingConventions'],
options['outputFile'], speciesEquivalence=options['userStructure'],
atomize=options['atomize'], bioGrid=False, pathwaycommons=options['pathwaycommons'])
if namespace.bionetgen_analysis and returnArray:
ls2b.postAnalyzeFile(options['outputFile'], namespace.bionetgen_analysis, returnArray.database)
def main():
parser = defineConsole()
namespace = parser.parse_args()
options = checkInput(namespace)
returnArray = ls2b.analyzeFile(options['inputFile'], options['conventionFile'], options['useId'], options['namingConventions'],
options['outputFile'], speciesEquivalence=options['userStructure'],
atomize=options['atomize'], bioGrid=False, pathwaycommons=options['pathwaycommons'], ignore=options['ignore'], noConversion = options['noConversion'])
if namespace.bionetgen_analysis and returnArray:
ls2b.postAnalyzeFile(options['outputFile'], namespace.bionetgen_analysis, returnArray.database)
if namespace.annotation and returnArray:
with open(options['outputFile'] + '.yml', 'w') as f:
f.write(yaml.dump(returnArray.annotation, default_flow_style=False))
def main():
parser = defineConsole()
namespace = parser.parse_args()
options = checkInput(namespace)
returnArray = ls2b.analyzeFile(
options["inputFile"],
options["conventionFile"],
options["useId"],
options["namingConventions"],
options["outputFile"],
speciesEquivalence=options["userStructure"],
atomize=options["atomize"],
bioGrid=False,
pathwaycommons=options["pathwaycommons"],
ignore=options["ignore"],
noConversion=options["noConversion"],
memoizedResolver=options["memoizedResolver"],
replaceLocParams=options["replaceLocParams"],
quietMode=options["quietMode"],
logLevel=options["logLevel"],
obs_map_file=options["obs_map_file"],
)
if namespace.bionetgen_analysis and returnArray:
ls2b.postAnalyzeFile(
options["outputFile"],
namespace.bionetgen_analysis,
returnArray.database,
replaceLocParams=options["replaceLocParams"],
)
if namespace.annotation and returnArray:
with open(options["outputFile"] + ".yml", "w") as f:
f.write(yaml.dump(returnArray.annotation,
default_flow_style=False))