Save auto-flexibilized enzymes during generate_protModels pipeline

[alinarekena]

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Description of the new feature:

flexibilizeProteins is called from constrainEnzymes when generating proteome-constrained ecModels. In flexibilizeProteins, second round of flexibilization of abundances is carried out as part of generate_protModels pipeline. The first round of modifications from around lines 124-125 of generate_protModelsare saved as an output, while those from flexibilizeProteins are only shown in command window.

I hereby confirm that I have:

• [+] Done this analysis in the master branch of the repository
• [+] Checked that a similar issue does not exist already

[mihai-sysbio]

@alinarekena thanks for raising this feature request. Would this be something you would find comfortable to implement? There are some instructions regarding this process in the Contributor guidelines.

[alinarekena]

@mihai-sysbio thanks for your response. No, I can't do it myself.

[mihai-sysbio]

Thanks for letting us know - I'll let @IVANDOMENZAIN take it from here.

[edkerk]

In GECKO3 pipeline, flexibilizeProtConcs gives flexData output.