kimrutherford
commented
2 years ago I'd prefer to make a new file in the one line per gene format because otherwise we'll need to change the ortholog reading code. That file (pombe-cerevisiae-orthologs-with-systematic-ids.txt.gz) is the one read into JaponicusDB. That's why the file was created.
I think we should put the new file here: https://curation.pombase.org/dumps/latest_build/ rather than in the exports directory because that's where the equivalent human file lives.
pombe-cerevisiae-orthologs-with-systematic-ids.txt.gz and pombe-human-orthologs-with-systematic-ids.txt.gz are in the same format - one line per ortholog, using systematic IDs for all organisms. I think it makes sense to keep them in the same format. And it's a useful format for parsing.
ValWood
Make the table here: https://curation.pombase.org/dumps/latest_build/exports/ the same format as the human table (one line per pombe gene)
Then I need to check diff between the old and the new file https://www.pombase.org/data/orthologs/ (this is the file I create manually)
Historically I used to make a list of changes in the track wiki, and make a release once there were a bunch of changes. I think since the wiki disappeared I have been making the changes in artemis, (but not recording them in track).
If I can check that the files all line up we can move to the automated file export. The only reason I kept using the old version was because it had information about the tandem repeats. I think this info could just go in a README file....