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pombase / pombase-chado

PomBase code for accessing Chado
MIT License
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log file alleles not beginning with a gene name #1159

Closed ValWood closed 7 months ago

ValWood commented 8 months ago

I thought that this file only provided entries which did not match a gene name OR a synonym?

but I see that sam3 rad24 SPAC8E11.02c aee38813cc53380f is reported even though sam3 is a synonym?

Can this restriction be added?

kimrutherford commented 8 months ago

Hi Val. The code does check for alleles starting with synonyms but currently there has to be something after the gene name or synonym. If the allele name was "sam3-a1" it wouldn't appear in the logs.

Should I change the code?

ValWood commented 8 months ago

That makes sense. I couldn't figure out the criteria because I knew that quite a few alleles used synonyms but weren't in the logs.

Keep it as it is for now.

I think some of these are recorded as pka1-sam3 and I have aligned with this syntax for some sessions, which would probably be a better solution, and will not violate.

kimrutherford commented 7 months ago

Should we keep this open?

ValWood commented 7 months ago

no can close. this file is almost cleaned up!

https://curation.pombase.org/dumps/latest_build/logs/log.2024-04-21-21-08-46.chado_checks.AlleleNotStartingWithGeneName