[Bioperl-l] Bio::AlignIO::po

[Matthew Betts]

Hi Jason / Heikki,

Thanks for the advice. I've submitted the code and tests via bugzilla (bug 
1606)

Hope this is useful,

Matthew


On Tue, 23 Mar 2004, Heikki Lehvaslaiho wrote:

> Matthew,
> 
> The list does not accept attachments. 
> 
> The recommended way of submitting new code is to open a bioperl bugzilla entry 
> and label it "enhancement" (in "Severity"): http://bugzilla.bioperl.org/. Put 
> the code into an attachment and a mail to bioperl-l list to discuss it.
> 
> 
> Thanks,
> 
> 	-Heikki
> 
> On Tuesday 23 Mar 2004 16:13, Matthew Betts wrote:
> > Hi,
> >
> > I've finally written the Bio::AlignIO:po module I mentioned way back in
> > November. I'm unsure of the procedure for submitting it (I've looked at
> > the FAQ). Should I just post it as an attachment to bioperl-l?
> >
> > Also, I'm trying to think of some sensible tests, and have been looking at
> > AlignIO.t. The ones in there mainly seem to test that a sequence read in
> > from an example alignment has the correct name. Should I test more than
> > that? All suggestions very welcome.
> >
> > Thanks in advance for your help,
> >
> > Matthew
> >
> > On Thu, 13 Nov 2003, Jason Stajich wrote:
> > > One does not exist - would be happy for you to write one.
> > > AlignIO::clustalw or fasta would be good templates.
> > > An AlignIO pir parser wouldn't be too bad either if you get into it.
> > >
> > > -jason
> > >
> > > On Thu, 13 Nov 2003, Matthew Betts wrote:
> > > > Hei,
> > > >
> > > > Does anyone have a PO format reader for AlignIO? This is the native
> > > > output format for POA. It can also output in pir or clustalw, so it's
> > > > not a big problem. But I'd quite like to try to try my hand at writing
> > > > the parser if one doesn't exist already...
> > > >
> > > > Thanks,
> > > >
> > > > Matthew
> > >
> > > --
> > > Jason Stajich
> > > Duke University
> > > jason at cgt.mc.duke.edu
> 
> 

-- 
Matthew Betts, mailto:matthew.betts at ii.uib.no
Phone: (+47) 55 58 40 22, Fax: (+47) 55 58 42 95
CBU, BCCS, HiB, UNIFOB / Universitetet i Bergen
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