ArnaudBelcour / MeneTools

MeneTools are Python3 tools to explore the topology of metabolic networks. It includes Menecheck, Menescope, Menepath and Menecof.

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 or pip install pyasp --no-cache-dir in case of ASP solvers installation issues)

Install

python setup.py install

There are some known issues with the pyasp package. If obtaining such an error when running a Menetool:

OSError: Grounder '/.../lib/python3.4/site-packages/pyasp/bin/gringo4' not found

It means that the binaries were not correctly installed for pyasp. These two command lines should be an efficient workaround:

1. uninstall pyasp pip uninstall pyasp
2. reinstall pyasp without cache pip install pyasp --no-cache-dir

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

from menetools import run_menecheck

model = run_menecheck(draft_sbml='required',seeds_sbml='required',targets_sbml='required')

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

from menetools import run_menescope

model = run_menescope(draft_sbml='required',seeds_sbml='required')

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

from menetools import run_menescope

model = run_menepath(draft_sbml='required',seeds_sbml='required',targets_sbml='required',min_size='optional',enumeration='optional')

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

from menetools import run_menecof

model = run_menecof(draft_sbml='required',seeds_sbml='required',targets_sbml='required',cofactors_txt='optional',weights='optional',suffix='optional',enumeration='optional')