Command Line Tweaks and Starting PhyInit.pl

I have been slightly modifying the command line arguments I initially suggested to make the arguments consistant with the existing BioSQL related scripts. (ie --dbuser in addition to -u will be valid arguments). This will require that I use Getopt::Long. I am also trying to decide if I want to mix caps in with the command line (ie. should it be PhyInit.pl, phyinit.pl, OR phy_init.pl). These are pretty minor issues but something I want to make consistant with the prexisting bioperl code.

After looking through the exising BioSQL code, I really like the idea of defaulting many of the command line variables to environmental variables, for example

 my $usrname = $ENV{DBI_USER};
 my $pass = $ENV{DBI_PASSWORD};

This is a somewhat obvious thing to do in retrospect, but not something that I have done before.

On the project page I have been going through the existing code in the codebase that is relevant to my proposed programs and linking to the locations of the code in CVS. I was wanting to finish this up tonight, but it looks like the wg_phyloinformatics wiki is down for the evening.

I have started the PhyInit.pl program and will make my first commit to subversion tonight. This will not be a finished program, but I want to be in the practice of making commits on a daily basis as much as possible.