Scott Cain's website

Bioinformatics, Perl, Cool Stuff
Powered by Drupal, an open source content management system


scott's blog

I went to see a house in Oberlin for my aunt and uncle who'd like to move back to Ohio. Pictures will be along later, but until then, here are a few youtube videos of the house:



Over the course of the last week, I:

  • Update the update_featureloc function to allow for "fuzzy" matching, which will allow for a few indels and base changes. (2 hours)
  • Tested the new update_featureloc function. All but 22 features passed; those 22 will be examined by hand (2 hours)
  • Ran and committed the full update (minus the 22 featureloc failures) so that Rob can begin testing (1 hour)

Wrote update_featureloc() (2 hours)
Started testing update_featureloc() (1.5 hours)

Tested the update_featureprop and update_analysis functions on the test database, and while they work (that is, they run and generate results), I'll have to spend a little more time with it to make sure that it really works: for one thing, there are no instances where the annotation symbol is updated. That could be because it doesn't need it, or because the function doesn't work right for that term; I'll have to write some queries to see if that is the case.

1 hour

Wrote the update_analysis function that updates both the analysis and the analysisfeature tables. (1 hour)

Worked on updating featureprops with annotation symbols; crafted a query to do it but I'm not sure it will work as planned (won't know until I try it on real data) (0.5 hour)

Started writing update_featureprop function. Currently handles the generic case and the tiling_path_fragment case (1.5 hours) and started on the annotation_symbol case (0.5 hours)

  • Did testing on the Janelia dev database and minor fixes to the code to this point (0.5 hour)
  • Wrote function for updating feature_status_history (0.5 hour)

Wrote update_feature_synonym, which included creating the synonym table entry, plus making a pub entry for the feature_synonym row.

Writing update_feature_synonym(): 1 hour
Testing update_feature_synonym(): 0.5 hour

Wrote update_feature_cvterm: 1.5 hours
testing: 0.5 hour.

Forgot that I'd have to worry about pub_ids when migrating the feature_cvterm rows, so it took a little longer than I'd expected.