[Bioperl-l] Phred.pm, Consed.pm, Trim.pm, Primer3.pm

Chad Matsalla matsallac@EM.AGR.CA
Fri, 03 Aug 2001 11:54:04 -0400

Hi all,

I expect to be allowed to release several modules within a couple of
weeks. A already asked for help with a couple of them but here is a list
of what I would like submit:

Consed.pm - Create and work with componene.ace files including
   consensus sequences and sequence qualities.
Trim.pm - A module that Consed.pm uses to screen consensus
  sequences for quality failures.
Phred.pm - Parse phred files and make objects of called bases and
Primer3.pm - Use primer3 to create primersets and parse output files from

I have a couple of questions:
1. The modules @ISA Bio::Root::RootI and throw exceptions through RootI.
Do I just commit this into CVS and get somebody to tell me if I did things
2. What should the modules be called? ie Where should they go? I currently
call them things like CSM::Consed and CSM::Phred because I'm CSM.
3. How do I submit them? Can you give me CVS write access?
4. There are some open() calls and other stuff that may or may not be
platform dependent. Can somebody help with this?

I think I would just like to commit them and gladly take criticisms.


Chad Matsalla
Agriculture & Agri-Food Canada
Saskatoon, Saskatchewan, Canada