[Bioperl-l] back to the grind of 0.7

Hilmar Lapp hlapp@gmx.net
Fri, 15 Dec 2000 10:59:40 -0800

Ewan Birney wrote:
> (2) More fun stuff.
> Refactor Bio::Seq set to be more flexible for other formats.
> I am going to proprose a class
>          Bio::Seq::GenEMBL
> which derives off Bio::Seq, and has extensions for GenEMBL stuff, being
> the date, sv etc etc stuff. Does this sound ok?

Sounds very ok :-)

In addition, if no-one else has done it already, over the weekend I'm
going to delete documentation of the deprecated methods (Seq::ary()

> I don't think we need separate GenBank/EMBL classes as the information in
> the files are pretty concordant (of course, if someone wants to help me
> with ASN.1 parsing into this, join the party!)

I wrote an email to info@ncbi.nlm.nih.gov asking for a pointer to
documentation of viewer.cgi mentioned by Lewis Geer, but no response
yet. So, it might be that XML support is not in a productive state yet.

> (3) See what I can get out of Keith's PSU code into bioperl.
> Sounds good? Hilmar - how are we doing - there aren't many green lights on
> the task list, but I think that's because we haven't updated the Wiki...

Sounds good. Just updated the task list. We're doing okay I think. There
may not be many greens, but there are some other colors than only red.
In a sense we're behind schedule, but given the fact that this is a
volunteer-only game and most of us appear to be heavily involved in
their primary jobs, I'm not worried as long as the table keeps changing
(and a red-shift is by definition excluded :-) If we hadn't Jason on
board, things would look significantly worse. He's been the driving
force code-wise so far.


Hilmar Lapp                                email: hlapp@gmx.net
GNF, San Diego, Ca. 92122                  phone: +1 858 812 1757