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

[Jason Stajich]

On Tue, 23 Mar 2004, 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?
>
(hmm - guess we need someone to add some more stuff to the FAQ...)

posting to bioperl-l is fine, but the preferred way is of you to submit
it at bugzilla.open-bio.org as a feature request and attach the module as
an attachment/patch where bugzilla allows that (I think only after you
have created the bug can you do that).  This lets the core developers see
if anyone else has already dealt with committing the module.  Also - we
probably will just give you CVS access once you've shown you know your way
around the toolkit.

> 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.

more, better tests are better.  people in the past have been lazy about
making tests which really test things to the max.  We probably should
have lots more tests in AlignIO.t - just need someone willing to write
some more in.

As many tests as you think can reasonably show that things are getting
parsed correctly, your data structures are coming out properly etc.  This
is important so that if someone goes in and screws up something in your
code or something that it depends on - we'll know that your parser/writer
isn't working correctly.


-jason

>
> 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
> >
>
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu