[Bioperl-l] Bio::AlignIO::metafasta tests

Chris Fields cjfields at uiuc.edu
Tue Jun 6 10:36:16 EDT 2006


Heikki,

I agree it's all a bit weird.  Not too concerning at the moment though since
it works at the moment but it might take some tinkering with SimpleAlign to
get it to behave.

This alignment format has some of the same characteristics as Stockholm
alignment format but looks easier to work with.  I work with RNA,
specifically one with a conserved secondary structure so this format appeals
to me quite a bit.  If I get time (probably not for a while) I may tinker
with Bio::AlignIO::stockholm to get a write_aln() method up-and-running and
see if I can convert back-and-forth from the two.

Chris

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Heikki Lehvaslaiho
> Sent: Tuesday, June 06, 2006 2:40 AM
> To: bioperl-l at lists.open-bio.org
> Cc: Chris Fields
> Subject: Re: [Bioperl-l] Bio::AlignIO::metafasta tests
> 
> Chris,
> 
> I am mystified. I'll try to get the massive 'return undef' change done
> first
> and the have an other look.
> 
> 	-Heikki
> 
> On Friday 02 June 2006 21:13, Chris Fields wrote:
> > Heikki,
> >
> > I uncovered a weird bug concerning Bio::AlignIO::metafasta which popped
> up
> > when running AlignIO.t (I was fixing bug 2000):
> >
> > http://bugzilla.open-bio.org/show_bug.cgi?id=2016
> >
> > Not sure what's going on there but using read_aln and write_aln seem to
> > work normally.  It may have something to do with Bio::SimpleAlign but
> I'm
> > not absolutely sure.
> >
> > Any ideas what may be going on here?
> >
> > Christopher Fields
> > Postdoctoral Researcher - Switzer Lab
> > Dept. of Biochemistry
> > University of Illinois Urbana-Champaign
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> --
> ______ _/      _/_____________________________________________________
>       _/      _/
>      _/  _/  _/  Heikki Lehvaslaiho    heikki at_sanbi _ac _za
>     _/_/_/_/_/  Associate Professor    skype: heikki_lehvaslaiho
>    _/  _/  _/  SANBI, South African National Bioinformatics Institute
>   _/  _/  _/  University of Western Cape, South Africa
>      _/      Phone: +27 21 959 2096   FAX: +27 21 959 2512
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