Installation

To install Flutopy with its dependencies:

conda install flutopy -c cfrioux -c potassco -c bioconda -c ibmdecisionoptimization

See https://github.com/cfrioux/fluto for documentation

Dependencies:

Pyasp ( conda install -c bioconda pyasp)
Cplex for python (conda install -c ibmdecisionoptimization cplex provides a promotional version sufficient to solve the toy example) Use python setup.py install --force to overwrite the promotional version with the academic one
Clingo ( conda install -c potassco clingo)

Usage

python fluto.py -h

usage: fluto.py [-h] -m MODEL [-r REPAIRBASE] [-s SEEDS] [-e]

Performs hybrid (topological/flux) gap-filling

optional arguments:
-h, --help            show this help message and exit
-m MODEL, --model MODEL
                    organism metabolic model in SBML format
-r REPAIRBASE, --repairbase REPAIRBASE
                    database of reactions for gap-filling
-s SEEDS, --seeds SEEDS
                    topological seeds to unblock circular dependencies in
                    the graph. Txt file with one seed ID per line
-e, --export          enabling export of compounds to prevent metabolite
                    accumulation

requires Python Clingo, PyASP and Cplex packages. See README and INSTALL

Toy example

Available on https://github.com/cfrioux/fluto

python fluto.py -m data/toy/draft.xml -s data/toy/toposeeds.txt -r data/toy/repairdb.xml