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GoekeLab / xpore

Identification of differential RNA modifications from nanopore direct RNA sequencing
https://xpore.readthedocs.io/
MIT License
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data-prep genome mapping for species other than homo sapiens #17

Closed sbultmann closed 4 years ago

sbultmann commented 4 years ago

Hi! Thank you for this great tool. It seems to be working flawlessly in my hands. I only have a small comment: At the moment dataprep.py only accepts an ensmbl release number and no species. When using data mapped to non-human genome, this causes the transgene to gene mapping to fail silently resulting in an empty data.json. I think it could be an easy fix (if I haven't missed anything ;-) ) by adding another option to the get_args():.

Something like: required.add_argument('--species', dest='species', help='species for ensembl gene-transcript mapping.', default='homo_sapiens)

in def main(): adding: ensembl_species = args.species

and changing line 516 to: ensembl = EnsemblRelease(ensembl_version, ensembl_species)

Anyway thanks a lot for this tool and the preprint!

ploy-np commented 4 years ago

Thank you very much Sebastian. I'll include it in the next release soon.

ploy-np commented 4 years ago

I fixed this and updated it to version 0.5.1 already. Thank you again for your suggestion.