Metadata-Version: 1.1
Name: MeneTools
Version: 1.0.0
Summary: Metabolic Network Topology Tools. Analyze the topology                         of metabolic networks. Explore producibility, production                         paths and needed initiation sources
Home-page: https://github.com/cfrioux/MeneTools
Author: Clemence Frioux
Author-email: clemence.frioux@gmail.com
License: GPLv3+
Download-URL: https://github.com/cfrioux/MeneTools/tarball/1.0.0
Description: # 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
        ```
        
Platform: UNKNOWN
