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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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Add possibility of using TD GFF3 files instead of the BED files, for loading the longest ORFs #55

Closed lucventurini closed 8 years ago

lucventurini commented 8 years ago

This is due to the fact that TransDecoder does not create the BED file during LongOrf, but only a GFF3 file. This will require a separate parsing.

lucventurini commented 8 years ago

This is probably less useful than it sounds - initial testing on Arabidopsis indicated a decrease in performance by Mikado, not an increase

lucventurini commented 8 years ago

This has become trivial since the Transcript objects now support conversion to BED12. Although inelegant, it is possible to create BED12 objects simply with:

orf_object = BED12(transcript.format("bed12")).

The utility of doing so seems very limited though. Ignoring and closing for now.