Feature #521
closed
Convert gff_getevidence_map.py to use flatfile instead of MySQL
Description
This is the only remaining step of the genome processing that uses MySQL queries. If we want to be able to send processing jobs out to virtual machines, it should just needs some links to files, not a local MySQL instance. Also, these MySQL queries are slow, too, changing this is likely to greatly speed up this processing step (currently around 30-40% of total). Another cases of removing MySQL queries sped up processing nearly 40-fold (23968b27)
Probably the thing to do is use "latest-flat.tsv", which should be regularly generated by a cron job from the GET-Evidence MySQL database.
Related issues
Updated by Ward Vandewege about 13 years ago
- Blocking changed from #426 to issue #426
Updated by Ward Vandewege about 13 years ago
- Blocking changed from issue #426 to 426
Updated by Madeleine Ball about 13 years ago
- Status changed from In Progress to Resolved
- Resolution set to fixed
Fixed by commit 940417cc
Non-substitution amino acid changes are still broken (variants will show up as insufficiently evaluated because no GET-Evidence match was found), but otherwise works fine.