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SysBioChalmers / GECKO

Toolbox for including enzyme constraints on a genome-scale model.
http://sysbiochalmers.github.io/GECKO/
MIT License
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runDLKcat(): use DLKcat.tsv in a different directory #392

Closed edkerk closed 1 month ago

edkerk commented 1 month ago

Discussed in https://github.com/SysBioChalmers/GECKO/discussions/389

Originally posted by **PkiwiBird** August 8, 2024 It is possible to modify the directory where _DLKcat.tsv_ is stored, with: `writeDLKcatInput(ecLiverMl,[],[],[],'path_2_light_DLKcat.tsv',true)` but how to use that file as input for `runDLKcat()` ? This is useful if we want to save the files of _DLKcat.tsv_ for the full and light models separately, as they are different. `runDLKcat()` uses `modelAdapter.params`. Is there a way to run `runDLKcat()` using as input _DLKcat.tsv_ stored in a different directory than `modelAdapter.params`?
edkerk commented 1 month ago

runDLKcat has the filename and path hard-coded in the python command to run DLKcat. It should indeed be possible to tell runDLKcat which file to use as an input (and the output file as well). This can be implemented, but it will take a little while before I have time to do this.

As a workaround you could use MATLAB's movefile command to rename the input file just before running runDLKcat, and rename it again after runDLKcat is done.

edkerk commented 1 month ago

@pkiwibird, does the modified runDLKcat in #394 work for you?