Seq.pm / etc.

[Georg Fuellen]

Updates on Aln.pm are linked to at
http://www.techfak.uni-bielefeld.de/bcd/Perl/Bio/welcome.html
In particular, the test program works well now, and the docu
has just been extended. Feedback appreciated ! More soon !

> 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.

Ok! Do you think we can announce Seq.pm ? (I would have time for testing
next weekend, I hope.)

> 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.

Yep; as you can see from http://www.techfak.uni-bielefeld.de/bcd/Perl/Bio/welcome.html
We'll very soon have 2 mailing lists; vsns-bcd-perl (this one), and
vsns-bcd-perl-announce. Steve: Can you update the CPAN info ?

> 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.

There will soon be support for module bundling (this was discussed on the
perldl mailing list), so we should definitely go for seperate modules, and
bundle them as soon as this is supported (5.004 I believe)

> 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.

That would be nice ! I've got my first script almost working, but some
bug with the color setup still needs to be worked at.

> 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 ]

I'm still struggling with this myself, e.g. with the Fasta RegExp, but I hope
I've got that one fixed next week !

best wishes,
georg

> 
>