[Bioperl-l] on BP documentation

[Chris Fields]

On Aug 15, 2009, at 6:17 AM, Bernd Web wrote:

> Hi
>
>>>   Even SeqIO is hard
>>> to figure out now--it took me an hour the other day to figure out  
>>> that
>>> "desc" returns the full Fasta header, and I had to get that from the
>>> module code + trial-and-error, instead of the online docs.
> I was a bit surprised about $seq->desc retrieving the entire FASTA  
> header line
> Actually, in Bioperl 1.52 at least $seq->desc returns the description
> only, so without the ID. Thus, to get the entire FASTA header line
> $seq->id . " " $seq->desc would be needed.

Odd, not seeing where a change was made that would cause this  
behavior.  Can you post an example?

> For the modules I use (mainly related to sequences, such as SeqIO,
> SimpleAlign), I'd be happy to contribute on docs, checking docs, or
> examples.
>
> Regards,
> Bernd

Would be nice to have an Align/SimpleAlign HOWTO, but seeing as we  
want to refactor large chunks of that code, it might be slightly  
premature.  That is, unless we want to document what behavior we  
expect to see as a sort of ROADMAP (maybe as part of the refactoring  
page).  That could then be converted over to a HOWTO.

Feel free to chip in on this in any way possible.  The more  
documentation the better.

chris