findCPcli

findCP CLI package


Keywords
modelling, metabolism, cobrapy, metabolic-models, sbml, metabolic-network, genome-scale, dead-end, chokepoint, fva
Licenses
GPL-3.0/GPL-3.0+
Install
pip install findCPcli==0.1.0

Documentation

findCPcli

standard-readme compliant

Source

Table of Contents

Install

$ pip install findCPcli

Run

$ findCPcli [-h] [-v] -i <input file> [-o <output file>]
                 [-cp <output file>] [-swD <output file>] [-sF <output file>]
                 [-swDF <output file>]

                       
optional arguments:
  -h, --help           show this help message and exit
  -v, --verbose        Print feedback while running.
  -i <input file>      Input metabolic model. Allowed file formats: .xml .json
                       .yml
  -o <output file>     Output spreadsheet file with results. Allowed file
                       formats: .xls .xlsx .ods
  -cp <output file>    Output spreadsheet file with chokepoints sensibility
                       analysis. Allowed file formats: .xls .xlsx .ods
  -swD <output file>   Save output model without Dead End Metabolites. Allowed
                       file formats: .xml .json .yml
  -sF <output file>    Save output model with reactions bounds updated with
                       Flux Variability Analysis. Allowed file formats: .xml
                       .json .yml
  -swDF <output file>  Save output model with reactions bounds updated with
                       Flux Variability Analysis and without Dead End
                       Metabolites. Allowed file formats: .xml .json .yml

Maintainers

@alexOarga

Contributing

Feel free to dive in! Open an issue or submit PRs.

Standard Readme follows the Contributor Covenant Code of Conduct.

License

MIT © Alex Oarga