Bio::Seq / Steve's comments

[Chris Dagdigian]

Steve - I recieved your mailed comments a few days ago, thanks!

I'm planning to translate steve's notes into a specific list of changes to
make to Seq.pm and I'll post the list (along with some questions) to the
mailing list.

Making a separate Readseq.pm module seems to be fairly high up on the
priority list and would allow me to clean up parts of Seq.pm. I'd be
willing to write a simple version that uses temporary files instead of
bidirectional piping. The one part I would need guidance on would be the
interface -- I'm too new to OO/Module work to trust myself with designing
the most functional set of methods.

On a similar note, Brian Osborne bas noted that he uses the seqio package
for parsing because ReadSeq doesn't handle large genomic sequences (>
100000 bp) that well - If we come up with a good interface for Readseq.pm
it would be easiy to create a seqio.pm as well.

Would those go in Bio::Parse or Bio::Util or something? I really am quite
new at dealing with modules and such :)


Regards,
Chris Dagdigian