Module for converting metabolic networks into Answer Set Programming (ASP) and more
Pip requirements are in requirements.txt.
Companion module of aspefm.
mparser_cli.py: Allows conversion of networks between various formats, command line interface
mparser_gui.py: Allows conversion of networks between various formats, graphical user interface (requires PySimpleGui)
aspsmatrix.py: Extracts and pickles the matrix from the mparser-read matrix, also contains many legacy functions
parse_and_check_output.py: More advanced version of aspefm/parse_output.py using the kernel test on the aspsmatrix matrix to check validity of solutions
thermo_csv.py: Short script converting a csv of keq values into an ASP file. See data folder for thermo data.
prepare_efm_checker.py: Script preparing the input file for aspefm/extensions/efm_checker.py based on the aspsmatrix matrix.
add_sbml_boundaries.py: Script converting COBRA SBML files into non-COBRA SBML files with added boundary metabolites in the most outer compartment.
Some of these scripts contain legacy functions, which may not be still functional today.
Implements conversion from METATOOL format and SBML format to ASP and more. Found in the mparser folder.
The file global_parameters.py is meant as a file gathering all global parameters that are not given in argument to mparser_cli.py and mparser_gui.py.
SBML to network reading parameters are by default adapted to COBRA files, which are not necessarily representative of every possible SBML.
The file compress_model.py contains code from CNAPy Team's EFMTool_Link, which might require Java and the jdk. Make sure to install all requirements.
python mparser_cli.py METATOOL data/ppp.txt ASP data/ppp.lp4
python mparser_cli.py METATOOL data/ppp.txt SBML data/ppp.xml
python mparser_cli.py SBML data/ppp.xml ASP data/ppp_dual.lp4 --to-dual-mcs --target-reactions R_ALD
python prepare_efm_checker.py $cobrafile.xml $cobrafile.efmc
python parse_and_check_output.py $file.txt $file.efms --check $sbmlNetwork --pickle $file.pkl --sbml