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Metabolic Network Completion. Compute minimal completions to your draft network with reactions from a repair network.

Project description

Installation

You can install meneco by running:

$ pip install --user meneco

On Linux the executable script can then be found in ~/.local/bin

and on MacOS the script is under /Users/YOURUSERNAME/Library/Python/3.2/bin.

Usage Command line interface

Typical usage is:

$ meneco.py -d draftnetwork.sbml -s seeds.sbml -t targets.sbml -r repairnetwork.sbml

For more options you can ask for help as follows:

$meneco.py --h
usage: meneco.py [-h] -d DRAFTNET -s SEEDS -t TARGETS [-r REPAIRNET]
                 [--enumerate]

optional arguments:
  -h, --help            show this help message and exit
  -d DRAFTNET, --draftnet DRAFTNET
                        metabolic network in SBML format
  -s SEEDS, --seeds SEEDS
                        seeds in SBML format
  -t TARGETS, --targets TARGETS
                        targets in SBML format
  -r REPAIRNET, --repairnet REPAIRNET
                        perform network completion using REPAIRNET a metabolic
                        network in SBML format
  --enumerate           enumerate all minimal completions

Usage Library

For a guided example, see a demonstration IPython Notebook.

Samples

Sample files for the reconstruction of ectocarpus are available here: ectocyc.sbml, metacyc_16-5.sbml, seeds.sbml, targets.sbml

Project details


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Filename, size & hash SHA256 hash help File type Python version Upload date
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