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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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[BUG] Mikado prepare forgets the phases of the CDS of input transcripts #133

Closed lucventurini closed 5 years ago

lucventurini commented 5 years ago

When a coding transcript with a truncated ORF at the 3', ie with a non-0 starting phase, passes through Mikado prepare, the program sets that phase to 0 arbitrarily. This should be repaired before the release is finalised.

lucventurini commented 5 years ago

The problem stems from the fact that - stupidly - I am not storing the CDS phases in the load_into_storage function (Mikado.prepare.annotation_parser). This is the section that has to be fixed for mikado prepare to function properly.

lucventurini commented 5 years ago

Unit test added and all checks passed. Closing.

lucventurini commented 5 years ago

Solved the corner cases that were causing sparse failures. Closing for now, although we might want to give the option to adjust the start for CDSs (comparatively with what we do with TransDecoder) in the future.