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

Hilmar Lapp hilmarl@yahoo.com
Sat, 04 Aug 2001 23:51:03 +0200

Chad Matsalla wrote:
> 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
>    qualities.
> Primer3.pm - Use primer3 to create primersets and parse output files from
>    primer3.
> 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
> correctly?

Sure. Commit it and someone will check it out.

> 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.

I agree with Ewan: Bio::Assembly::*

> 3. How do I submit them? Can you give me CVS write access?

>From what I can see you already have it. Do you know your login?

> 4. There are some open() calls and other stuff that may or may not be
> platform dependent. Can somebody help with this?

The tests on other platforms will usually uncover those
dependencies. That is, it'd be great if you can submit test
scripts, too (see examples in t/*.t), otherwise could you submit
at least sample input files (then someone else might jump in and
code the test scripts).


Hilmar Lapp                              email: hilmarl@yahoo.com