[Bioperl-l] on BP documentation

Amir Karger akarger at CGR.Harvard.edu
Mon Aug 17 09:04:29 EDT 2009

> -----Original Message-----
> From: Mark A. Jensen [mailto:maj at fortinbras.us]
> From: "Hilmar Lapp" <hlapp at gmx.net>
> ...
> > As for the FASTA example, I can understand - I've heard
> repeatedly
> > from people that one of the things that they are missing is
> > documentation for every SeqIO format we support  (such as
> GenBank,
> > UniProt, FASTA, etc) about where to find a particular piece of
> the
> > format in the object model.
> This is the right thread for list lurkers to contribute their betes
> noires
> such as this one. I encourage ALL to post these issues and help
> create
> our list of action items.

I wish you the best of luck on this ambitious and crucial project. I
teach intro Perl classes to biologists and always tell them that Bioperl
is amazingly useful, but only if you can figure out how to use it. If
what you want to do isn't in the howtos, you can be in big trouble.

I was trying to remember specific examples of where I've gotten lost,
and unfortunately can't give any. But I can tell you that often I've run
into trouble because the particular method I'm looking for is three
parent classes away from the module I'm actually looking at. The
deobfuscator helps some, but only for people who know about that. Do you
think you could automate a tool that would add the following to the
bottom of each module?

=head2 Inherited methods

=over 4

=item desc

See Bio::Seq::Basic


This would make browsing through the docs on bioperl.org more fun too.

-Amir Karger

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