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StrainDesign

Github Version Conda Version
GitHub Super-Linter Coverage
License DOI Code style: black Gitter

Description

straindesign provides a cli interface to predict gene knockout targets with an heterologous pathway. Integrate an hard fork from cameo (v0.13.6) named cameobrs to add features.

Installation

conda install -c bioconda straindesign

Usage

Define the best combination of genes deletion to optimize a target

python -m straindesign simulate-deletion \
    [input files]
    --input-model-file <SBML file>
    --input-pathway-file <SBML file>
    --input-medium-file <CSV/TSV file>
    [parameters]
    --biomass-rxn-id <id reaction, str>
    --target-rxn-id <id reaction, str>
    --substrate-rxn-id <id reaction, str>
    [output file]
    --output-file <CSV/TSV file>

Delete genes in a model

python -m straindesign reduce-model \
    [input files]
    --input-model-file <SBML file>
    --input-straindesign-file <CSV file>
    and/or
    --input-gene-str <id gene, str>
    [parameters]
    --parameter-strategy-str <yield-max, gene-max, gene-min>
    [output file]
    --output-file-sbml <SBML file>

You can provide a list of genes to delete in the model or the file produced by the command simulate-deletion. If this file is provided, the combination of genes is choosen among three strategies:

  • yield-max: genes are sorted by the best yield
  • gene-max: the combination of the maximum number of genes
  • gene-min: the combination of the minimum number of genes

Produce a pareto plot

python -m straindesign analyzing-model \
    [input files]
    --input-model-file <SBML file>
    --input-medium-file <CSV/TSV file>
    --input-pathway-file <SBML file>
    [parameters]
    --biomass-rxn-id <id reaction, str>
    --target-rxn-id <id reaction, str>
    --substrate-rxn-id <id reaction, str>
    [output file]
    --output-pareto-png <PNG file>

You can provide an heterologous pathway to implement the metabolic pathway producing the targeted compound represented by the target-rxn-id, the reaction which produces this compound.
The substrate-rxn-id argument lets you to choose the main carbon source.

Tests

Requires:

  • pytest
  • pytest-benchmark
python -m pytest

straindesign's People

Contributors

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straindesign's Issues

deprecated `iteritems`

Warning:

iteritems is deprecated and will be removed in a future version. Use .items instead.

in flux_variability_based.py

Use Jupyter standard platformdirs

Warning:

DeprecationWarning: Jupyter is migrating its paths to use standard platformdirs given by the platformdirs library.  To remove this warning and see the appropriate new directories, set the environment variable JUPYTER_PLATFORM_DIRS=1 and then run jupyter --paths.
The use of platformdirs will be the default in jupyter_core v6
 from jupyter_core.paths import jupyter_data_dir

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