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openvax / pyensembl

Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl
Apache License 2.0
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Add an exception for Saccharomyces cerevisiae in `is_valid_ensembl_id(ensembl_id)` function #209

Closed rraadd88 closed 6 years ago

rraadd88 commented 6 years ago

Hello developers, I experienced errors when I tried to work with Saccharomyces cerevisiae genome using pyensembl. I could install the genome successfully. But a function called is_valid_ensembl_id(ensembl_id) disallows me from doing any more than installing the genome. It is located at https://github.com/openvax/pyensembl/blob/4e2af0a00b10702fbc6e0ba66bafca79a2031d2c/pyensembl/common.py#L87

I would imagine it would be a quick fix to add an exception for Saccharomyces cerevisiae genome. In case of yeast, the gene ids (unconventionally) start with 'Y' eg. YHR055C, YPR161C, YOL138C etc.

I hope you would be able to incorporate this in the next release.

(Also, I saw that the current build is failing which is disconcerting. :/ ) Thank you.