v2 isocreatealign code omits residues from certain genes

sheynkman-lab / biosurfer

"Surf" the biological network, from genome to transcriptome to proteome and back to gain insights into human disease biology.

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v2 isocreatealign code omits residues from certain genes #43

Closed jsaquing closed 3 years ago

jsaquing commented 3 years ago

Alignments affected:

ARHGEF1-203|204
ICAM4-202|201
OSCAR-204|206

Occurs at exon junctions.

jsaquing commented 3 years ago

fixed by https://github.com/sheynkman-lab/biosurfer/commit/4d35715de4320fc9c62e314cb97ff10f927dc9c3

gsheynkman commented 3 years ago

For how many genes did you confirm the bug fix works on? I think these exon-boundary-residue cases are edge cases that can crop up but in rare genes.

jsaquing commented 3 years ago

The bug only affected those three genes in the sample set. I feel pretty confident that I fixed that specific problem in the code, but of course there could be other bugs that just don't show up for the sample genes. I suppose we could try comparing the old and new versions of the alignment code on a larger set of genes (like chr22) to really make sure their outputs are identical?

gsheynkman commented 3 years ago

I think that would be a good idea.