Protein feature viewer: special case rpb1

[ValWood]

http://dev.pombase.kmr.nz/gene_protein_features/SPBC28F2.12

we have special allele naming syntax for the rpb1 (and another protein?)
@manulera can poit you to this. These will be 'conjoined' alleles

(not necessary for release)

[kimrutherford]

we have special allele naming syntax for the rpb1 (and another protein?)

The allele parsing for amino_acid_mutation is very simple at the moment. There are quite a few that are ignored. I've been meaning to chat about it on a call.

rpb1 has descriptions like these that are ignored:

• https://www.pombase.org/genotype/rpb1-CTD-S5.S5A-%28CTD%29S5A%28alternating%29-amino_acid_mutation-expression-not_assayed_or_wild_type
• https://www.pombase.org/genotype/rpb1-CTD-S2A-%28CTD%29S2A-amino_acid_mutation-expression-not_assayed_or_wild_type
• https://www.pombase.org/genotype/rpb1-CTD-S2A%285-16%29,CTDdelta%2817-29%29-CTD-S2A%285-16%29,CTDdelta%2817-29%29-amino_acid_deletion_and_mutation-expression-not_assayed_or_wild_type

spt5 also has some that are ignored:

• https://www.pombase.org/genotype/spt5-%28CTD%29T1A%287%29-%28CTD%29T1A%287%29-amino_acid_mutation-expression-not_assayed_or_wild_type
• https://www.pombase.org/genotype/spt5-%28T1A%297-CTD-T1A-amino_acid_mutation-expression-not_assayed_or_wild_type

[manulera]

Yes, rpb1 and spt5 are the CTD ones, for now those should be ignored.

[kimrutherford]

Is this covered by?:

• protein modification errors pombase-chado#1141

[ValWood]

Similar, this ticket is for the alleles ...

[ValWood]

do not do until
pombase/pombase-chado#1192

[kimrutherford]

The seems a bit more challenging than the modifications because of alleles like this:

• rpb1-CTD-S2A(5-16),CTDΔ(17-29)(CTD-S2A(r5-r16),delta(r17-r29))

[ValWood]

true, we can skip these for now, because this is really a "partial deletion and amino acid change", and up to now we don't display alleles of that type for any gene

[kimrutherford]

OK, we should have a chat about this sometime and decide which of these to show:
https://www.pombase.org/gene_alleles/SPBC28F2.12