Python selectReactionDefinitions示例

示例#1

文件： sbmlTranslator.py 项目： RuleWorld/PyBioNetGen

def checkInput(namespace):
    options = {}
    options["inputFile"] = namespace.input_file

    conv, useID, naming = ls2b.selectReactionDefinitions(options["inputFile"])
    options["outputFile"] = (namespace.output_file if namespace.output_file
                             is not None else options["inputFile"] + ".bngl")
    options["conventionFile"] = (namespace.convention_file
                                 if namespace.convention_file is not None else
                                 conv)
    options["userStructure"] = namespace.user_structures
    options["namingConventions"] = (namespace.naming_conventions
                                    if namespace.naming_conventions is not None
                                    else naming)
    options["useId"] = namespace.molecule_id
    options["annotation"] = namespace.annotation
    options["atomize"] = namespace.atomize
    options["pathwaycommons"] = namespace.pathwaycommons
    options["bionetgenAnalysis"] = namespace.bionetgen_analysis
    options["isomorphismCheck"] = namespace.isomorphism_check
    options["ignore"] = namespace.ignore
    options["noConversion"] = namespace.convert_units
    options["memoizedResolver"] = namespace.memoized_resolver
    options["replaceLocParams"] = not namespace.keep_local_parameters
    options["quietMode"] = namespace.quiet_mode
    options["obs_map_file"] = namespace.obs_map_file
    assert namespace.log_level in [
        "CRITICAL",
        "ERROR",
        "WARNING",
        "INFO",
        "DEBUG",
    ], "Logging level {} is not an allowed level".format(namespace.log_level)
    options["logLevel"] = namespace.log_level
    return options

示例#2

文件： __main__.py 项目： arfeenkhalid/parameter-synth

def checkInput(namespace):
    
    options = {}
    options['inputFile'] = namespace.input_file
    
    conv,useID = ls2b.selectReactionDefinitions(options['inputFile'])    
    options['outputFile'] = namespace.output_file if namespace.output_file != None else options['inputFile'] + '.bngl'
    options['conventionFile'] = namespace.convention_file if namespace.convention_file != None else conv
    options['userStructure'] = namespace.user_structures
    options['useId'] = namespace.molecule_id
    options['atomize'] = namespace.atomize
    options['biogrid'] = namespace.biogrid
    return options

示例#3

文件： sbmlTranslator.py 项目： cihankayacihan/bionetgen

def checkInput(namespace):
    
    options = {}
    options['inputFile'] = namespace.input_file
    
    conv,useID,naming = ls2b.selectReactionDefinitions(options['inputFile'])    
    options['outputFile'] = namespace.output_file if namespace.output_file != None else options['inputFile'] + '.bngl'
    options['conventionFile'] = namespace.convention_file if namespace.convention_file != None else conv
    options['userStructure'] = namespace.user_structures
    options['namingConventions'] = namespace.naming_conventions if namespace.naming_conventions != None else naming
    options['useId'] = namespace.molecule_id
    options['atomize'] = namespace.atomize
    options['pathwaycommons'] = namespace.pathwaycommons
    return options

示例#4

文件： sbmlTranslator.py 项目： elihuihms/bionetgen

def checkInput(namespace):

    options = {}
    options['inputFile'] = namespace.input_file

    conv, useID, naming = ls2b.selectReactionDefinitions(options['inputFile'])
    options[
        'outputFile'] = namespace.output_file if namespace.output_file != None else options[
            'inputFile'] + '.bngl'
    options[
        'conventionFile'] = namespace.convention_file if namespace.convention_file != None else conv
    options['userStructure'] = namespace.user_structures
    options[
        'namingConventions'] = namespace.naming_conventions if namespace.naming_conventions != None else naming
    options['useId'] = namespace.molecule_id
    options['atomize'] = namespace.atomize
    options['pathwaycommons'] = namespace.pathwaycommons
    return options

示例#5

文件： sbmlTranslator.py 项目： RuleWorld/atomizer

def checkInput(namespace):
    options = {}
    options['inputFile'] = namespace.input_file

    conv, useID, naming = ls2b.selectReactionDefinitions(options['inputFile'])
    options['outputFile'] = namespace.output_file if namespace.output_file is not None else options['inputFile'] + '.bngl'
    options['conventionFile'] = namespace.convention_file if namespace.convention_file is not None else conv
    options['userStructure'] = namespace.user_structures
    options['namingConventions'] = namespace.naming_conventions if namespace.naming_conventions is not None else naming
    options['useId'] = namespace.molecule_id
    options['annotation'] = namespace.annotation
    options['atomize'] = namespace.atomize
    options['pathwaycommons'] = namespace.pathwaycommons
    options['bionetgenAnalysis'] = namespace.bionetgen_analysis
    options['isomorphismCheck'] = namespace.isomorphism_check
    options['ignore'] = namespace.ignore
    options['noConversion'] = namespace.no_conversion
    return options

示例#6

def checkInput(namespace):
    options = {}
    options['inputFile'] = namespace.input_file

    conv, useID, naming = ls2b.selectReactionDefinitions(options['inputFile'])
    options[
        'outputFile'] = namespace.output_file if namespace.output_file is not None else options[
            'inputFile'] + '.bngl'
    options[
        'conventionFile'] = namespace.convention_file if namespace.convention_file is not None else conv
    options['userStructure'] = namespace.user_structures
    options[
        'namingConventions'] = namespace.naming_conventions if namespace.naming_conventions is not None else naming
    options['useId'] = namespace.molecule_id
    options['annotation'] = namespace.annotation
    options['atomize'] = namespace.atomize
    options['pathwaycommons'] = namespace.pathwaycommons
    options['bionetgenAnalysis'] = namespace.bionetgen_analysis
    options['isomorphismCheck'] = namespace.isomorphism_check
    options['ignore'] = namespace.ignore
    options['noConversion'] = namespace.no_conversion
    return options