Missing scaffold genes

I use pyensembl for gene id/name mapping but lately I noticed that some ensembl gene ids (e.g. ENSG00000285395) are missing in pyensembl.EnsemblRelease(97).genes().

That’s I think because pyensembl is using {species}.{reference}.{release}.gtf.gz GTF URL template instead of {species}.{reference}.{release}.chr_patch_hapl_scaff.gtf.gz (see https://ftp.ensembl.org/pub/release-97/gtf/homo_sapiens/ for comparison).

I understand that this file includes genes that are not mapped to chromosomes, so might be problematic in the context of pyensembl, but still, it’d be more complete to include all the genes.

[iskandr]

Thanks for pointing this out. Do you think it’s OK to just include the scaffold names as if they were chromosomes or do they need further special treatment?

Also, do you think that their inclusion in the results of genes() should be the default or optional?

[fabianegli]

I would say it is desirable to have specific logic in the code to cope with release versions of databases since they can change more than once which can result in a failure!=failure scenario.

Another reason to use database version specific path pattern hardcoding is that they are not expected to change and thus the hardcoding of path patterns serves a documentation purpose, too.

The last point would be performance - a try-except block might be slightly faster but loading a file is much slower than a case switch and/or path generation and thus I expect the performance difference of different selection methods to be negligible.