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tgen / bisbee

alternative splicing analysis pipeline
MIT License
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Mouse ensembl ids incompatible with prot/utils.py #3

Open jamyers2358 opened 3 years ago

jamyers2358 commented 3 years ago

Line 180 of prot/utils.py truncates mouse ensembl ids. Current code: transcript_ids=ensembl.transcript_ids_of_gene_id(gene_id[0:15]) This will result in all of your ensembl Ids to be "not found". To overcome this you can replace with this: transcript_ids=ensembl.transcript_ids_of_gene_id(gene_id.split('.')[0]) which will be compatible with both human and mouse IDs.

Priyatham-sai-chand commented 3 years ago

Changing the same in except to have clear error message is also useful.

https://github.com/tgen/bisbee/blob/d12ded4e4ee497e18a8b8e4929dac0e08de9f7f6/prot/utils.py#L180-L182