Week 2 Project update

Below is the weekly progress report email I sent to the Wg-phyloinformatics listserv.

Hi All --

Week 2 Update for: Command Line Topological Query Application for BioSQL

Last week:
* Updated project web page:
- to reflect changes in command line options
- linked to SVN source
- linked to existing code that is relevant to what I am working on
* Modified my original command line options to fit the standards used in the existing BioSQL scripts
* Wrote PhyInit.pl to initialize the phylogenetic data tables for BioSQL
- This currently assumes an existing BioSQL database
- DB handle info can be sent as:
(1) dsn string as ENV variable,
(2) dsn string at command line,
(3) separate command line vars (--host,--driver,--dbname) that are used to create dsn string
- A new DB will be created if a DB with the name in the dsn string does not exist
() This uses the --dbname or a series of split commands to get info from command line --dsn
() SQL create table code is hard coded in MySQL format
- Password can be entered in a 'secure' fashion if not passed at the command line.
* Given an existing DB, only the new tables will be created, existing tables will be deleted
- User is warned before deleting any existing data. This step does a record count to tell the user how many records would be deleted from any existing tables.
* Started PhyImport.pl to import phylogenetic data from NEXUS,Newick files
- Mainly just set up command line options and POD documentation
* Posted changes I made to the schema to get this to work in MySQL on the project code repository
* All new PERL code was place in the project working repository listed below
* The -h or --help command line switch can be used to read POD documentation

This week:
* PhyImport.pl
- Add NEXUS file support
- Add Newick file support
* PhyInit.pl
- Check over POD documentation
- Add ability to use sql in the sqldir, this will create the full BioSQL schema if needed

Project Web: https://www.nescent.org/wg_phyloinformatics/PhyloSoC:Command_Line_Topological_Query_Application_for_BioSQL
Project blog: http://phylosoc2007jestill.blogspot.com
Working repository: http://code.google.com/p/phylosoc2007jestill