Seq.pm / etc.

[Chris Dagdigian]

Hi all,

 I've made the following changes in Seq.pm:

  - dup() has been fixed and renamed copy()
  - parse_gcg() was added (in a very basic form)
  - _type() was removed because its functionality was duplicated
    by _monomer(), origin() and type()

 The code and POD is available at http://www.ayf.org/~c_raffi/bioperl/
 I will hopefully have an anonymous FTP site available soon.


Now for some thoughts:

The CPAN module list still has Bio::* listed as "i" which classifies us as
being in an "idea" or "placeholding" stage. We need to update that
classification to "a/b" for alpha/beta testing (or "C" for
under-construction). Steve is the only one who can change this as he is the
registered author.

Perhaps we can also add our list to the CPAN description of perl-related
mail lists.

I fully agree with Georg's comments that most of the value of Seq.pm will
come from a robust system for parsing/output. I also thing that the Bio::*
distribution should consist of different directories. Focusing on providing
tools that make it easier to use perl as a 'glue' language is a smart way
to go.

As for the WWW/CGI/Graphics push that Georg mentioned, I have many perl
scripts that use Lincoln Stein's CGI.pm as a user interface. We've writen
CGI front-ends to almost all of the GCG/EGCG utilities as well as for
various other programs that our scientists find useful. At a later date
maybe we can all clean up our various scripts and put out a Bio::Util
distribution containing many useful CGI's.

Regards,
Chris Dagdigian

[ Regular expressions are not my strongest area :) and generally at work I
only deal with fasta and GCG formatted sequence formats. I would welcome
and appreciate any help or suggestions on creating parsing and output code
for various biosequence formats ]