Sampling Biomarker Analysis using flux sampling
Project description
SAMBAflux
Description
SAMpling Biomarker Analysis is a python package for running flux sampling on metabolic networks. Once installed, it can be imported into new python scripts or used with scripts from the SAMBA repository.
Visuals
[add example plots here]
Getting started
Requirements
- Python 3.7
- cobrapy
- A solver (GLPK, CPLEX, GUROBI)
- Access to a computer cluster or powerful computer when sampling larger models
Installation
Install via pip:
pip install sambaflux
Usage
-h, --help show this help message and exit
-m MODEL, --model MODEL
Metabolic model. Supported file formats: SBML, json, mat.
-n NSAMPLES, --nsamples NSAMPLES
The number of samples
-p PROCESSORS, --processors PROCESSORS
Number of processors
-t THINNING, --thinning THINNING
The thinning factor of the generated sampling chain. A thinning of 10 means samples are returned every 10 steps.
-o OUTPATH, --outpath OUTPATH
Outfile path (without filename)
-k KO, --ko KO KO file containing reactions to KO, specify nothing if you want to sample WT
-s SEPKO, --sepko SEPKO
Separator for the KO file
-r RESULTS, --results RESULTS
File containing reactions to output, specify nothing if you want only exchange reactions
-q, --quiet Use this flag to silence INFO logging.
-d, --debug Use this flag to turn on DEBUG logging.
--dryrun Use this flag to run the code without running sampling.
--log LOG Log file path + filename. Set to None to output to console.
-b BIOMASS, --biomass BIOMASS
Number between 0 and 1, fraction of biomass to optimize
--solver {cplex,gurobi,glpk}
Solver to use
--exchangemin EXCHANGEMIN
The value used to set the minimum flux through exchange reactions (will be negative). Set to None if you want the default exchange reaction bounds.
--biomassrxn BIOMASSRXN
A .tsv containing a Model column with the name of models and a Biomass column with the name of the corresponding biomass reaction.
-f, --fva Use this flag to run FVA as well as sampling.
--onlyfva Use this flag to run FVA instead of sampling.
See here for set-up and usage with the project's scripts.
Authors
Juliette Cooke
Acknowledgments
License
MIT License (see LICENSE file)
Project status
Currently active on this project.
Project details
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