MENETOOLS MeneTools are Python3 tools to explore the topology of metabolic network to: - assess whether targets are topologically producible (Menecheck) - get all compounds that are topologically producible (Menescope) - get production paths of specific compounds (Menepath) - obtain compounds that if added to the seeds, would ensure the topological producibility of targets (Menecof) Required package: pyasp (pip install pyasp) Install: python setup.py install ——————————————————————————————————————————————————————————————————————————————— ——————————————————————————————————————————————————————————————————————————————— MENECHECK Menecheck is a python3 tool to get the topologically producibility status of target compounds usage: menecheck.py [-h] -d DRAFTNET -s SEEDS -t TARGETS 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 ——————————————————————————————————————————————————————————————————————————————— MENESCOPE Menescope is a python3 tool to get the topologically reachable compounds from seeds in a metabolic network. usage: menescope.py [-h] -d DRAFTNET -s SEEDS 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 ——————————————————————————————————————————————————————————————————————————————— MENEPATH Menepath is a python3 tool to get the topologically essential reactions with respects to individual targets in metabolic networks. usage: menepath.py [-h] -d DRAFTNET -s SEEDS -t TARGETS 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 ——————————————————————————————————————————————————————————————————————————————— MENECOF Menecof is a python3 tool to get the minimal set of cofactors that enables to maximize the number f producible targets. Study of the metabolic network is made` topologically using reachable compounds from seeds. usage: python menecof.py [-h] -d DRAFTNET -s SEEDS -t TARGETS [-c COFACTORS] [--suffix SUFFIX] [--weight] [--enumerate] the following arguments are required: -d/--draftnet, -s/--seeds, -t/--targets optional arguments: --suffix --weight --enumerate -h/--help -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 -c COFACTORS, --cofactors COFACTORS cofactors, in one-per-line text file format --suffix SUFFIX suffix to be added to the compounds of the database. It can be the suffix for the cytosolic compartment or external one. Cytosolic one is prefered to ensure the impact of the added cofactors. Default = None --weight call this option if cofactors are weighted according to their occurrence frequency in database. If so, cofactors file must be tabulated with per line compound' 'occurrence --enumerate enumerates all cofactors solutions
lrivallain/MeneTools
MeneTools are Python3 tools to explore the topology of metabolic networks. It includes Menecheck, Menescope, Menepath and Menecof.
Python