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japonicusdb / japonicus-curation

Data files for JaponicusDB
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Orthologs to add #22

Closed ValWood closed 3 years ago

ValWood commented 3 years ago

following from: https://github.com/japonicusdb/japonicus-config/issues/32#issuecomment-879018983

add to japonicus manual orthologs file. Then GO annotation will come automatically.

ACTION: ORTHOLOGS TO ADD

Check that GO annotation propagates

ValWood commented 3 years ago

@kimrutherford Do we have a place to do this yet? I can't remember! If so where?

kimrutherford commented 3 years ago

All the files are here: https://github.com/japonicusdb/japonicus-curation

If the orthologs are for pombe, you probably want to edit: https://github.com/japonicusdb/japonicus-curation/blob/main/manual_pombe_orthologs.tsv

ValWood commented 3 years ago

I edit in the editor. I add tabs, but it looks like this:

Screenshot 2021-07-14 at 11 56 27

Is that OK? It definitely looks like it should only be a single tab when I'm editing?

Also what format for one to many? I used: SJAG_03542 SPBC8D2.03c|SPAC1834.03c|SPBC1105.12 SJAG_00303 SPBC8D2.03c|SPAC1834.03c|SPBC1105.12

kimrutherford commented 3 years ago

I edit in the editor. I add tabs, but it looks like this:

The new lines have 2 spaces instead of a tab.

Also what format for one to many?

Currently it only supports one pair per line like: SJAG_03542 SPBC8D2.03c|SPAC1834.03c|SPBC1105.12 SJAG_03542 SPBC8D2.03c|SPAC1834.03c|SPBC1105.12 SJAG_03542 SPBC8D2.03c|SPAC1834.03c|SPBC1105.12

kimrutherford commented 3 years ago

Sorry, make that: SJAG_03542 SPBC8D2.03c SJAG_03542 SPAC1834.03c SJAG_03542 SPBC1105.12

kimrutherford commented 3 years ago

Let's do command line Git workshop sometime. Alternatively, GitHub have a desktop Git application you could use: https://desktop.github.com/

ValWood commented 3 years ago

Let's do command line Git workshop sometime.

Yes please!

ValWood commented 3 years ago

I fixed to this format, but I can't prevent the weird formatting. SJAG_03542 SPBC8D2.03c SJAG_03542 SPAC1834.03c SJAG_03542 SPBC1105.12

kimrutherford commented 3 years ago

I've fixed the formatting.