Include N/C flags in ortholog export files for fusion proteins

kimrutherford commented 3 months ago

We need to show clearly in the export ortholog when a pombe gene is a fusion. Maybe like this?:

SPAC806.02c     YIL003W(N)|YDR267C(C)

Or maybe this would make it more obvious that these are not 1-many orthologs?:

SPAC806.02c     YIL003W(N)+YDR267C(C)

kimrutherford commented 3 months ago

How does this format look? Should we put "N-term" / "C-term" in the brackets or is it clear enough?

SPCC1450.15     YBR265W(N)+YDR302W(C)
SPBC1711.13(C)  YCL030C
SPBC29A3.02c(N) YCL030C
SPAC22A12.08c   YDL142C(C)+YKR070W(N)
SPAC806.02c     YDR267C(C)+YIL003W(N)
SPBC16A3.11     YDR419W(N)+YFR027W(C)
SPAC22E12.10c   YER141W(N)+YPL252C(C)
SPBC530.12c     YGR036C(C)
SPBP4H10.15     YJL096W(C)+YJL200C(N)
SPAC2C4.12c     YJR067C(C)+YOL102C(N)
SPAC6F12.05c    YJR142W(N)+YOR143C(C)
SPAC1420.04c    YKL155C(N)+YPL132W(C)
SPAC19B12.13    YKL155C(N)+YPL132W(C)
SPAC15E1.04     YOR074C(C)
SPCC1223.08c    YOR236W(C)+YOR280C(N)
SPAC1002.01     YPL041C
SPAC1002.02     YLR018C
SPAC1002.03c    YBR229C
SPAC1002.04c    YML015C
SPAC1002.05c    YJR119C
SPAC1002.06c    NONE
SPAC1002.07c    YEL066W|YPR193C
SPAC1002.08c    YMR228W
SPAC1002.09c    YFL018C
SPAC1002.10c    NONE
SPAC1002.11     YLR088W
SPAC1002.12c    YBR006W
SPAC1002.13c    YIL123W|YJL116C|YKR042W|YNL066W
SPAC1002.14     YML068W
...

kimrutherford commented 3 months ago

How does this format look? Should we put "N-term" / "C-term" in the brackets or is it clear enough?

I've committed this change so we can see if it works in tonight's load.

For human it looks like:

SPAC806.02c     HGNC:14280(C)+HGNC:8042(N)
SPAC22E12.10c   HGNC:2263
SPBC405.01      HGNC:4163
SPCC569.08c     HGNC:4163
SPBC530.12c     HGNC:9325(N)
SPAC1002.01     NONE
SPAC1002.02     NONE
SPAC1002.03c    HGNC:4138
SPAC1002.04c    HGNC:11544
SPAC1002.05c    HGNC:11114|HGNC:11115|HGNC:18039|HGNC:9886

The lines for SPAC22E12.10c, SPBC405.01 and SPCC569.08c don't have brackets yet. They should look OK once this issue is done:

pombase/curation#3733

kimrutherford commented 3 months ago

I think that's all working.

pombase / pombase-chado

Include N/C flags in ortholog export files for fusion proteins #1203