efmlrs package

Subpackages

• efmlrs.postprocessing package
  • Subpackages
    • efmlrs.postprocessing.decompressions package
      • Submodules
      • efmlrs.postprocessing.decompressions.deadend module
      • efmlrs.postprocessing.decompressions.null_space module
      • efmlrs.postprocessing.decompressions.one2many module
      • Module contents
  • Submodules
  • efmlrs.postprocessing.decompressing module
  • efmlrs.postprocessing.get_data module
  • Module contents
• efmlrs.preprocessing package
  • Subpackages
    • efmlrs.preprocessing.compressions package
      • Submodules
      • efmlrs.preprocessing.compressions.deadend module
      • efmlrs.preprocessing.compressions.echelon module
      • efmlrs.preprocessing.compressions.null_space module
      • efmlrs.preprocessing.compressions.one2many module
      • Module contents
  • Submodules
  • efmlrs.preprocessing.boundaries module
  • efmlrs.preprocessing.get_data module
  • efmlrs.preprocessing.mplrs_output module
  • Module contents
• efmlrs.util package
  • Submodules
  • efmlrs.util.convert_matrix module
  • efmlrs.util.data module
  • efmlrs.util.log module
  • Module contents

Submodules

efmlrs.post module

efmlrs.post.main(inputfile, outputfile, infofile, efmtool)

Main script of prostprocessing part of EFMlrs. Calls all other scripts. First output files are read and compressed efms are stored in a list. Then the decompressing process is started iteratively in reversed order compared to the formerly applied compressions and each compressed efm is being decompressed one after another. The deompressed efms are written to the user specified output file. :param inputfile: output containing compressed efms either form mplrs or efmtool :param outputfile: file in which uncompressed efms are written to :param infofile: file automatically created during compressions, containing all information for decompressions :param efmtool: paramter that indicates whether decompressions for mplrs or efmtool is being executed :return: None

efmlrs.post.start(inputfile, outputfile, infofile, efmtool)

Takes all parameters form commandline, checks if parameters are okay and calls main function if an error occurs an exception is raised and ends the program. :param inputfile: output containing compressed efms either form mplrs or efmtool :param outputfile: file in which uncompressed efms are written to :param infofile: file automatically created during compressions, containing all information for decompressions :param efmtool: paramter that indicates whether decompressions for mplrs or efmtool is being executed :return: None

efmlrs.post.start_from_command_line()

Entry point for prostprocessing EFMlrs. Contains all information and arguments for command line call. Calls start function. :return: None

efmlrs.pre module

efmlrs.pre.main(inputsbml, ignore_compartments, boundflag)

Main script of preprocessing part of EFMlrs. Calls all other scripts. Compressions are being done iteratively as long as compressions can be found. Loop breaks after one loop with no changes in length of metabolites or reactions. Writes uncompressed and compressed output files including additional versions of the sfile with integers (instead of fractions) to be compatible with efmtool. Writes compressed input file for mplrs algorithm. Writes info file that is needed for decompressions and log file that contains all information on the applied compressions.

Parameters:

• inputsbml – path to sbml input file that contains the metabolic model
• ignore_compartments – list of compartments to ignore
• boundflag – bool flag when additional bounds should be taken into account

Returns:

None

efmlrs.pre.start(inputsbml, ignore_compartments, bounds)

Takes all parameters from command line, checks if parameters are okay and if everything is fine initialises log file and calls main function if an error occurs an exception is raised and ends the program. :param inputsbml: path to sbml input file that contains the metabolic model :param ignore_compartments: list of compartments to ignore :param bounds: bool flag when additional bounds should be taken into account :return: None

efmlrs.pre.start_from_command_line()

Entry point for preprocessing EFMlrs. Contains all information and arguments for command line call. Calls start function. :return: None

Module contents