[Bioperl-l] Re: SeqIO::swiss.pm + "gsequence"

Lorenz Pollak lorenz@ist.org
Thu, 14 Sep 2000 15:49:12 +0200 (CEST)

hi everyone!

> 1) superfluous empty line after the seq (does this hurt according to the
> specs?)
> 2) empty GN line (again, does this hurt?)
> 3) truncation of the OS line (at least in some cases)
> 4) OC line not being written correctly (at least in some cases)
> An example is accession P25222 (SwissProt) (mentioned in bug report
> #168). I can provide the entry if you need it.
> Any volunteers for fixing those things? Lorenz, still enthusiastic?

ok, i can do that! (during the next 3-5 days) and yes, please provide some
examples for testing.

> The version present in the branch-06 seems to be more or less broken, at
> least with respect to output printing. The question is whether or not we
> can take over the version from main trunk. Lorenz, could you summarize
> the modules you had to fix or even add in order to get the parser work?

hmm, i don't remember all those changes very well (cvs log could be
helpful), but i'm rather sure that the main work took place only in
swiss.pm with no other affected modules...

There I have another question:

I would not have made any changes to swiss.pm if i were not working on my
sequence control program. I implemented functions to load a protein
sequence and then for editing all properties / annotations. Then when I
tried to implement save/saveas functions I saw the unfinished stage of
that module and worked on improving swiss.pm writing capabilities.

(btw: the next thing i encountered was that it was not possible to have
empty sequences, which is a bit a problem if you want to give the
possibility of entering a complete new sequence instead of loading
one. has this behavior changed in the meantime?)

And now I've noticed that there are some other people working on gui
programs that are built on top of bioperl or at least cooperate with
bioperl modules and those seem to be at a more mature stage than my

"gsequence" is written using Gtk/Perl and is intended for editing protein
sequences + properties, entering new sequences, calling some analysis
programs (blast,hmmer,...) and showing output from that. I'm not sure if
that is really useful for other people.

So I'm asking myself whether I should continue with my "gsequence" program
or rather join an other gui programming group (could merge some code).

Any comments? (anyone that has had a look on gsequence?)

kind regards,