# 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:
```Python
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](./examples/small_network.py)).
`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()`.
1. Through a generic wrapper:
```Python
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](http://doi.org/10.1093/bioinformatics/btn401)
## 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.
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