Tuesday, June 12, 2007

Week 3 Update Email

I am currently out of town for some wheat related work, below is the email update I sent out.

Week 3 project update: Command Line Topological Query Application for BioSQL

Last week I:
  • Made changes to MySQL phylo tables in the biosql-phylodb-mysql.sql (http://phylosoc2007jestill.googlecode.com/svn/trunk/sql/biosql-phylodb-mysql.sql) to get foreign keys working and to include recent changes in the biosql schema
  • Updated PhyInit.pl to include these schema changes
  • Completed a version of PhyImport that uses the TreeIO module of bioperl to import tree nodes and edges
  • Generated random trees to serve as test import trees for PhyImport
This week I will:
  • Figure out problems I am having importing NEXUS trees with PhyImport (something to do with my bioperl installation)
  • Add node and edge attribute information to PhyImport
  • Add tree root information to PhyImport
  • Begin PhyExport for whole tree export

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