yali1 and yali0 gene identifiers

[edkerk]

Instead of using the CLIB122-derived YALI0 gene identifiers, used the W29-derived YALI1 genes instead. This most likely constitutes a whole new reconstruction, to be tracked in a separate branch.

edit: instead of separate branch, @ChristianLieven has included Yali1 identifiers in the same model here.

• evaluate of the solution above is functioning well when loading model with RAVEN and COBRA
• identify if new Yali1 genes (absent from Yali0) code for new reactions

[ChristianLieven]

Hi @edkerk are CLIB122-derived IDs due to a re-annotation and hence entirely different ORFs than W29-derived or would it be possible to use gene annotation to map between them?

[edkerk]

@ChristianLieven see this supplementary table from the W29 genome paper for a mapping of CLIB122 to W29 ORFs, As you can see, some genes nicely map, while others are missing or new.

[ChristianLieven]

Thanks @edkerk I'll take a look!