fromOrganismName2ReactionsList.py

[noctillion]

Traceback (most recent call last):
File "pipeline/fromOrganismName2ReactionsList.py", line 222, in
gL.writeLineByLineToFile(geneFile, [gene, lAssociatedRxns], sep = '\t')
TypeError: writeLineByLineToFile() got an unexpected keyword argument 'sep'

[JanZrimec]

I hva the same error when running both via kegg code ' or via organism name (same as leads to choice of kegg code).

I am running this on windows.
It would be good to obtain an actual version specific list of dependencies - so those package version that enabled stable execution of the latest version of gpruler (e.g. at publication). This might also resolve the errors. Would it be possible to obtain this list?

[JanZrimec]

Package versions can be found in the history of the GPRuler_requirements.txt (Commits on Mar 8, 2021), which resolves above issues for me.

[mdifilippo]

As you correctly found, the GPRuler_requirements.txt includes the specific version of each package

[SalgadoSergio]

I have installed each package version that is in the GPRuler_requirements.txt (Commits on Mar 8, 2021) and I still have the same error (in windows and also in linux)

[mdifilippo]

Can you kindly try again now? because we have fixed a typo that remained within the genericLib library.

[SalgadoSergio]

Now it works, but I had to delete two "sep" that were still there. Thank you.

[SalgadoSergio]

I think that doesn't work properly. I am retrieving only the information for the genes in the file '_GeneId2Rxns.csv', but the other generated files are empty.