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