Monday, June 18, 2007

Week 4 Project Update

I spent most of last week out of town for a meeting so I have some catching up to do this week.

Last week:
  • Tried to get a more stable dsn parser to work by using DBI subfunction parse_dsn
  • Finished up PhyImport
  • Updated code to better fit with existing bioperl coding standards
  • Fixed my installation of bioperl (This was to get NEXUS file import working)
    • I am now working from bioperl-live
  • Committed biosql-phylodb-mysql.sql to biosql-schema CVS
    • This is my first commit to a group project :)
    • I hope bioperl converts to SVN soon
This week:
  • Finish PhyExport to export trees from the database to text files
  • Start PhyOpt by getting a precomputed nested sets working
  • Try to figure out if I really want to continue to use Bio::Tree or switch to Bio::Phylo
    • The Bio::Phylo object seems more rich but it is not a bioperl module

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