Scott Cain's website

Bioinformatics, Perl, Cool Stuff
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Email: sco...@scottcain.net

Blogs

Needed to fix TAIR's arabidopsis data before it could be loaded into chado; I reported the problems back to the curators at TAIR.

2 hours

Spent time prepping the database and setting up the load of maize data (which will run for several hours)

2 hours

Last week (week of 3/23):

  • Investigated the possibility of reuse of code written by Ed Lee for HHMI project. Verdict: won't happen, as there is too tight of a tie in with the confluence wiki.

5 hours

This week (so far):

  • Setting up Chado and loading with ontologies on genestage server

3 hours

  • Time spent on trying to get proxy set up for cvs/svn (still no resolution)
  • Created a postgresql user for me and created a database for seqfeature::store
  • Tried to populate said database, but need a svn checkout of bioperl

0.5 hours

  • Finished the fasta clean up script
  • Generated GFF from fasta using gmod_fasta2gff.pl
  • Added funtionality to the jgi2gff.pl so that the user can specify either Chado or SeqFeature::Store flavored GFF3

1 hour

Started work on a script to fixed flawed fasta files (for Bio::DB::Fasta, the lenght of all the lines except the last need to be the same length; JGI doesn't agree).

0.5 hour

Finished jgi2gff.pl and tried (and failed) to get an anonymous checkout of chado cvs.

1 hour

Worked on a script to produce GFF3 from jgi gff2. Works now except for converting CDS to polypeptide features.

2 hours

Time spent in preparations for "real work":

  • Teleconferences/planning meetings (1 hour)
  • Configuring laptop/VPN/various computer stuff (4 hours)

The past few days I've done lots of work on creating a template for a private chado schema.

  • Had the private primary key table use the public key's sequence so their would be no problem moving the data from private to public
  • Created indexes that mirror all of the normal indexes in the public schema
  • Added unique, foreign key and not null constraints that mirror the public schema as well
  • Added default values that mirror the public schema; there is currently a problem with this that, when the default value is zero and the field is the last in the list, it doesn't get created properly. I'm continuing to work on that.

Work done yesterday and today: 9 hours.