[Bioperl-l] (no subject)

Jason Stajich jason@chg.mc.duke.edu
Tue, 12 Dec 2000 16:15:48 -0500 (EST)

Chris -

We'd love to have your additions to the module(s) if they are general
purpose.  There are a couple of options depending on how deep you want to
wade into the bioperl code pool.  You can obviously make the changes you
need by inheriting from the Bio::SeqIO::genbank module and adding extra
functionality and going on your merry way at your own location.  If it is
general purpose functionality (better author parsing, fuzzy feature
location, etc) then we'd enjoy having it to be added to the main branch
because otherwise someone else has to write this eventually...  If you do
this, your coding needs to be additions/corrections to a recent version of
the module(s) checked out via cvs (see http://cvs.bioperl.org for info
if you haven't already).

You can send your changes as diffs to the list and someone with a
developer account can volunteer to make the changes - or probably more 
effective, send it to the release coordinator (as we are working towards
the 0.7 release of bioperl) Hilmar Lapp <hlapp@gmx.net>, or to the
bioperl  project coordinator Ewan Birney (birney@ebi.ac.uk), or to me.
Usually we will look over the code, bless it as okay, and commit it to the
main trunk.  

If you think you might be contributing more that 1 or 2 bug fixes to
the bioperl project, you could also consider becoming a bioperl developer
and getting an account on our development server.  If that suits your
fancy let Ewan know.

Glad to have you involved.


On Tue, 12 Dec 2000, Strassel, Chris wrote:

> Hi all,
> I've been learning the modules for parsing genbank records. Pretty
> impressive. I am about to make a couple of additions to provide some
> functionality I need, and wanted to ask a couple questions before I begin...
> I have seen some postings about parsing fuzzy locations for features, but I
> get the impression that this isn't a function that exists yet. Can anyone
> confirm?
> Same for sequence versions (i.e. the gene index number on the version line).
> The author line(s) are not currently parsed. Has anyone done/tried to do
> this? Comments would be appreciated.
> Finally, I am unsure about how to go about adding functionality.  Create my
> own objects that inherit from the bioperl objects? Add functions directly to
> the bioperl objects? Something else?
> Thanks in advance,
> Chris
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Jason Stajich
Center for Human Genetics
Duke University Medical Center