#207 QC: check whether allele names are unique genome wide

[Valerie Wood]

They might not be any, but we can disambiguate if we find out how many there are.

[Kim Rutherford]

Here's the list of allele names that are duplicated and the count of the number of times the name is used:

     name          count
git6-261                  2
wee1-50                   2
end4-507                  2
T42A                      2
abc1delta                 2
crm1-N1                   2
prp1                      2
heterozygous diploid      3
cdc22-M45                 3
K56R                      3
homozygous diploid        4
                        159
no_name                 559

And here are the uniquenames/identifiers of the alleles with duplicated names:

        name                 uniquename
heterozygous diploid   SPAC17H9.09c:allele-4
heterozygous diploid   SPAC4A8.12c:allele-2
heterozygous diploid   SPBC1289.03c:allele-2
crm1-N1                SPAC1805.17:allele-6
crm1-N1                SPCC663.03:allele-4
T42A                   SPBC428.16c:allele-31
T42A                   SPAC1565.06c:allele-4
cdc22-M45              SPAC1F7.05:allele-3
cdc22-M45              SPBC582.03:allele-7
cdc22-M45              SPBC11B10.09:allele-14
homozygous diploid     SPAC1D4.13:allele-3
homozygous diploid     SPAC22H10.07:allele-3
homozygous diploid     SPAC16E8.09:allele-3
homozygous diploid     SPBC21.05c:allele-3
git6-261               SPBC106.10:allele-13
git6-261               SPAC926.04c:allele-6
wee1-50                SPAC144.13c:allele-2
wee1-50                SPCC18B5.03:allele-2
abc1delta              SPBC2D10.18:allele-1
abc1delta              SPAC9E9.12c:allele-3
prp1                   SPBC6B1.07:allele-3
prp1                   SPAC29E6.02:allele-2
end4-507               SPAC688.11:allele-2
end4-507               SPAC4F10.15c:allele-3
K56R                   SPAC1834.04:allele-2
K56R                   SPBC8D2.04:allele-2
K56R                   SPBC1105.11c:allele-2

[Valerie Wood]

Good. Not too many.

I think we can resolve the K56R type, by always including the gene name in fron of these name types hht1-k56R etc

Some appear to be mistakes (I don't think wee1-50 is a true allele of swr1

The only one I can see which might be a problem right now is abc1 delete...I think that has been used twice as an allele name./ Maybe in this instance abc1 could be made a synonym of allele ybt1(delta) (the approved name for SPAC9E9.12c)

Looks like a Friday afternoon task for us to do the fixes first and take it from there.

[Valerie Wood]

crm1-N1 SPAC1805.17:allele-6
crm1-N1 SPCC663.03:allele-4
cdc22-M45 SPAC1F7.05:allele-3
cdc22-M45 SPBC582.03:allele-7
cdc22-M45 SPBC11B10.09:allele-14
git6-261 SPBC106.10:allele-13
git6-261 SPAC926.04c:allele-6
wee1-50 SPAC144.13c:allele-2
wee1-50 SPCC18B5.03:allele-2
prp1 SPBC6B1.07:allele-3
prp1 SPAC29E6.02:allele-2
end4-507 SPAC688.11:allele-2
end4-507 SPAC4F10.15c:allele-3

appear to be typos and will be fixed.

I guess these are not an issue anyway, as they have the unique name.
I will lower the priority to 1 and we can have a look in the future if any more have accumulated