[Bioperl-guts-l] [Bug 2016] Bio::Align::metafasta

bugzilla-daemon at newportal.open-bio.org bugzilla-daemon at newportal.open-bio.org
Tue Jun 13 00:20:43 EDT 2006


http://bugzilla.open-bio.org/show_bug.cgi?id=2016





------- Comment #15 from cjfields at uiuc.edu  2006-06-13 00:20 -------
(In reply to comment #14)
> (In reply to comment #12)
> > There is another issue here: how do we handle such data in the context of
> > converting alignments?  This is Bio::AlignIO, so we're dealing with sequence
> > alignment conversions, not non-sequence data, at least in relatio to
> > SimpleAlign.  Although the changes need to be made to SimpleAlign, my feeling
> > is that the meta data should be tossed when converting from metafasta to other
> > formats using AlignIO and SimpleAlign.
> 
> I think you missed the point. SimpleAlign can (and does) simply ignore the meta
> data. You don't have to throw it away. You can do whatever conversions you
> like, the sequences behave like normal, but they retain their metadata so its
> there if you want it.
> 
> So really, all that needs to be done is apply my patch, change the expected
> values in the test and update Bio::AlignIO.pm with your change to
> _guess_format (to make it pick up metafasta format).

The test file and Bio::AlignIO have been updated (actually, Bio::AlignIO has
been updated to include metafasta for a week or so now).  I get your point
about the meta data now; I didn't realize that the alignment was built using
Bio::Seq::Meta objects instead of Bio::LocatableSeq objects.  My fault for not
reading enough into it; when I read your response above about padding the gaps
I assumed (wrongly upon rereading everything) that you meant the meta data and
not the sequence data.  

Heikki, do you really want to keep the SimpleAlign changes or should we roll
them back and use Sendu's patch?  I personally am leaning towards Sendu's patch
of Bio::AlignIO::metafasta as it's more direct.


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