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EI-CoreBioinformatics / mikado

Mikado is a lightweight Python3 pipeline whose purpose is to facilitate the identification of expressed loci from RNA-Seq data * and to select the best models in each locus.
https://mikado.readthedocs.io/en/stable/
GNU Lesser General Public License v3.0
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Allow codon table to be set in mikado prepare #426

Closed swarbred closed 2 years ago

swarbred commented 2 years ago

The user selected codon usage table is currently only used in mikado serialise, therefore when CDS features are present in the mikado prepare input these are translated with the standard genetic code (even if an alt has been set) this results in models failing the validation and being removed

Would make sense for the selected codon table to be used in both serialise and prepare.

swarbred commented 2 years ago

NOTE This is an issue that will affect reat homology and reat prediction as in both cases models with CDS features are in the GFF input to prepare and there is no way to prevent the check for internal stops (at best strip_faulty_cds: true , will retain the model but then requires ORFs to be recalled)

ljyanesm commented 2 years ago

Dear @swarbred,

Can you confirm this is fixed in the main branch? There are 3 commits to this effect on that branch, if so. We can close this ticket once there's a new release.

Best,

swarbred commented 2 years ago

@ljyanesm Yes that's correct, thanks