def which(program): """returns path to an executable if it is found in the path""" fpath, fname = __split(program) if fpath: if __isfile(program) and __os.access(program, __os.X_OK): return program else: paths_to_search = __os.environ["PATH"].split(__os.pathsep) paths_to_search.extend((omelib_directory, ome_directory)) for path in paths_to_search: exe_file = __join(path, program) if __isfile(exe_file) and __os.access(exe_file, __os.X_OK): return exe_file if __os.name == "nt" and not program.endswith(".exe"): return which(program + ".exe") return None
def which(program): """returns path to an executable if it is found in the path""" fpath, fname = __split(program) if fpath: if __isfile(program) and __os.access(program, __os.X_OK): return program else: paths_to_search = __os.environ["PATH"].split(__os.pathsep) paths_to_search.extend((trnlib_directory, trn_directory)) for path in paths_to_search: exe_file = __join(path, program) if __isfile(exe_file) and __os.access(exe_file, __os.X_OK): return exe_file if __os.name == "nt" and not program.endswith(".exe"): return which(program + ".exe") return None
from __future__ import with_statement, absolute_import import sys from os import name as __name available_tests = ['unit_tests', 'solvers', 'flux_analysis', 'io_tests'] del __name from os.path import abspath as __abspath from os.path import join as __join from os.path import split as __split from os.path import sep as __sep cobra_directory = __abspath(__join(__split(__abspath(__file__))[0], "..")) cobra_location = __abspath(__join(cobra_directory, "..")) data_directory = __join(__split(__abspath(__file__))[0], "data") if not data_directory.endswith(__sep): data_directory += __sep salmonella_sbml = __join(data_directory, "salmonella.xml") salmonella_fbc_sbml = __join(data_directory, "salmonella_fbc.xml") salmonella_pickle = __join(data_directory, "salmonella.pickle") salmonella_reaction_p_values_pickle = __join(data_directory, "salmonella_reaction_p_values.pickle") ecoli_sbml = __join(data_directory, "iJO1366.xml") ecoli_pickle = __join(data_directory, "iJO1366.pickle") ecoli_mat = __join(data_directory, "iJO1366.mat") ecoli_json = __join(data_directory, "iJO1366.json") yersinia_sbml = __join(data_directory, 'Yersinia_pestis_CO92_iPC815.xml') yersinia_pickle = __join(data_directory, 'Yersinia_pestis_CO92_iPC815.pickle') __test_pickles = {'Salmonella_enterica': salmonella_pickle, 'Escherichia_coli': ecoli_pickle,
"""retrive local user settings""" from configparser import SafeConfigParser import os as __os from os.path import split as __split, join as __join, abspath as __abspath, \ isfile as __isfile from sys import modules self = modules[__name__] # define various filepaths trnlib_directory = __join(__split(__abspath(__file__))[0], "") trn_directory = __join(__abspath(__join(trnlib_directory, "..")), "") def which(program): """returns path to an executable if it is found in the path""" fpath, fname = __split(program) if fpath: if __isfile(program) and __os.access(program, __os.X_OK): return program else: paths_to_search = __os.environ["PATH"].split(__os.pathsep) paths_to_search.extend((trnlib_directory, trn_directory)) for path in paths_to_search: exe_file = __join(path, program) if __isfile(exe_file) and __os.access(exe_file, __os.X_OK): return exe_file if __os.name == "nt" and not program.endswith(".exe"): return which(program + ".exe") return None
"""retrive local user settings""" from ConfigParser import SafeConfigParser import os as __os from os.path import split as __split, join as __join, abspath as __abspath, \ isfile as __isfile from sys import modules self = modules[__name__] # define various filepaths omelib_directory = __join(__split(__abspath(__file__))[0], "") ome_directory = __join(__abspath(__join(omelib_directory, "..")), "") def which(program): """returns path to an executable if it is found in the path""" fpath, fname = __split(program) if fpath: if __isfile(program) and __os.access(program, __os.X_OK): return program else: paths_to_search = __os.environ["PATH"].split(__os.pathsep) paths_to_search.extend((omelib_directory, ome_directory)) for path in paths_to_search: exe_file = __join(path, program) if __isfile(exe_file) and __os.access(exe_file, __os.X_OK): return exe_file if __os.name == "nt" and not program.endswith(".exe"): return which(program + ".exe") return None
from __future__ import with_statement, absolute_import import sys from os import name as __name available_tests = ['unit_tests'] del __name from os.path import abspath as __abspath from os.path import join as __join from os.path import split as __split from os.path import sep as __sep from cobra.manipulation import initialize_growth_medium gim3e_directory = __abspath(__join(__split(__abspath(__file__))[0], "..")) gim3e_location = __abspath(__join(gim3e_directory, "..")) data_directory = gim3e_directory + "/data/" gim3e_directory += '/core/' salmonella_pickle = __join(data_directory, "salmonella_gem.pickle") ecoli_sbml = __join(data_directory, "E_coli_core_M9.xml") del __abspath, __join, __split, __sep def create_test_model(test_pickle=salmonella_pickle): """Returns a cobra model for testing. The default model is the version of the Salmonella enterica Typhimurium LT2 model published in Thiele et al. 2011 BMC Sys Bio 5:8, which has some updated metabolite KEGG id data for Schmidt et al. 2013 Bioinformatics test_pickle: The complete file name of a pickled cobra.Model or SBML XML file to be read. We currently provide Salmonella enterica Typhimurium and Escherichia coli core models whose paths are stored in cobra.test.salmonella_pickle
from __future__ import with_statement, absolute_import import sys from os import name as __name available_tests = ['unit_tests', 'solvers', 'flux_analysis', 'io_tests'] del __name from os.path import abspath as __abspath from os.path import join as __join from os.path import split as __split from os.path import sep as __sep cobra_directory = __abspath(__join(__split(__abspath(__file__))[0], "..")) cobra_location = __abspath(__join(cobra_directory, "..")) data_directory = __join(__split(__abspath(__file__))[0], "data") if not data_directory.endswith(__sep): data_directory += __sep salmonella_sbml = __join(data_directory, "salmonella.xml") salmonella_fbc_sbml = __join(data_directory, "salmonella_fbc.xml") salmonella_pickle = __join(data_directory, "salmonella.pickle") salmonella_reaction_p_values_pickle = __join( data_directory, "salmonella_reaction_p_values.pickle") ecoli_sbml = __join(data_directory, "iJO1366.xml") ecoli_pickle = __join(data_directory, "iJO1366.pickle") ecoli_mat = __join(data_directory, "iJO1366.mat") ecoli_json = __join(data_directory, "iJO1366.json") yersinia_sbml = __join(data_directory, 'Yersinia_pestis_CO92_iPC815.xml') yersinia_pickle = __join(data_directory, 'Yersinia_pestis_CO92_iPC815.pickle') __test_pickles = {
from __future__ import with_statement, absolute_import import sys from os import name as __name available_tests = ['unit_tests'] del __name from os.path import abspath as __abspath from os.path import join as __join from os.path import split as __split from os.path import sep as __sep from cobra.manipulation import initialize_growth_medium gim3e_directory = __abspath(__join(__split(__abspath(__file__))[0], "..")) gim3e_location = __abspath(__join(gim3e_directory, "..")) data_directory = gim3e_directory + "/data/" gim3e_directory += '/core/' salmonella_pickle = __join(data_directory, "salmonella_gem.pickle") ecoli_sbml = __join(data_directory, "E_coli_core_M9.xml") del __abspath, __join, __split, __sep def create_test_model(test_pickle=salmonella_pickle): """Returns a cobra model for testing. The default model is the version of the Salmonella enterica Typhimurium LT2 model published in Thiele et al. 2011 BMC Sys Bio 5:8, which has some updated metabolite KEGG id data for Schmidt et al. 2013 Bioinformatics test_pickle: The complete file name of a pickled cobra.Model or SBML XML file to be read. We currently provide Salmonella enterica Typhimurium