Python wrapper for efmtool

efmtool is a Java software for the enumeration of Elementary Flux Modes (EFMs) developed by Marco Terzer at ETH Zurich. This package provides a simple Python wrapper.

Installation

pip install efmtool

Usage

The wrapper provides two ways of calling efmtool:

1. Through a simplified interface:

   efms = efmtool.calculate_efms(
       stoichiometry : np.array,
       reversibilities : List[int],
       reaction_names : List[str],
       metabolite_names : List[str],
       options : Dict = None,
       jvm_options : List[str] = None)
   

   This function directly returns a NumPy array containing all the EFMs of the specified network (example). reversibilities is a list indicating whether a reaction is reversible (1) or not (0). Note that irreversibilities are assumed to be in forward directions. If a reaction is irreversible in the backward direction, it should be reversed before calling efmtool. Default options can be obtained through get_default_options().

2. Through a generic wrapper:

   efmtool.call_efmtool(
       args : List[str],
       jvm_options : List[str] = None)
   

   The wrapper simply calls efmtool passing the specified arguments. Specifying, writing and reading input/output temporary files is responsibility of the user.

See config/metabolic-efm.xml, the documentation, or run java -cp lib/metabolic-efm-all.jar ch.javasoft.metabolic.efm.main.CalculateFluxModes --help for more information about the available options.

Known issues

An (unknown) issue in the original Java software causes the wrapper to fail on operating systems with German/Austrian localization. If you obtain TypeError: buffer is too small for requested array consider switching to a language without diaeresis/umlaut in the month names (Jän, Mär, ...).

Cite us

If you use efmtool in a scientific publication, please cite our paper:

Terzer, M., Stelling, J., 2008. "Large-​scale computation of elementary flux modes with bit pattern trees". Bioinformatics. - link

Credits

efmtool is a software written by Marco Terzer (ETH Zurich).

Python wrapper by Mattia Gollub (ETH Zurich).

Thanks to Axel Theorell (ETH Zurich) for OSX compatibility fixes.