feat: specify carbon source with fermentation data

[edkerk]

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When generating multiple proteomics-constrained ec-models with different carbon sources, this currently would require different getModelParameters.m and fermentationData.txt files. Instead, in this PR:

• the carbon source exchange reaction name is included in fermentationData.txt

• load_Prot_Ferm_Data.m places this information in fermParameters.c_source

• generate_ProtModels.m uses the condition specific fermParameters.c_source instead of the information from getModelParameters. (It does not replace parameters.c_source in getModelParameters, as the carbon source mentioned here is specific for each proteomics dataset)

• some duplicated code (see line 25-27 and 37-39 in old file) was removed.

[codecov-io]

Codecov Report

Merging #134 (6165161) into devel (cfb6b99) will not change coverage. The diff coverage is n/a.

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  Files           3        3           
  Lines         200      200           
  Branches       22       22           
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  Hits          194      194           
  Misses          4        4           
  Partials        2        2           

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[edkerk]

Last thing to fix here, although not just related to using different carbon sources, is that if generate_protModels runs for multiple conditions is overwrites the model file in every iteration, in location models/prot_constrained/NAME/NAME.xml. If can think of three solutions, of which I now implemented the first option (commit 2f51995):

1. Rename the file in each iteration to models/prot_constrained/NAME/NAME_CONDITION.xml
2. Alternatively save the file and the additional tables in models/prot_constrained/NAME_CONDITION/NAME.xml and comparable.
3. Alternatively as 2, but only if the number of conditions > 1, otherwise save as models/prot_constrained/NAME/NAME.xml (as the original code).

(Also did a minor change of saveECmodel when toolbox 'RAVEN' is specified (commit 6165161), it now writes all model files in the same folder, same behaviour as COBRA),

[edkerk]

The changes intended here have been superseded by various developments as part of GECKO3.