[Bioperl-l] printing UnivAlgn

[Ewan Birney]

On Fri, 15 Dec 2000, Murad Nayal wrote:

> 
> 
> is UnivAln being phased out? if not then maybe it is worth it to make
> UnivAln conform to 'the SimpleAlign interface'. I am guessing this is
> probably a simple thing to do and would make at least AlignIO able to
> print either alignment object in all formats etc. 

Feel free to jump in and sort this out! (whoever codes it, wins the
argument...)

I agree with Peter tht we should focus efforts on one of them, which seems
to be SimpleAlign and move functionality into it. What do you use UnivAln
for?


> 
> Peter Schattner wrote:
> > 
> > Murad Nayal wrote:
> > 
> > > Hello,
> > >
> > > I can not find a straightforward way to get a SimpleAlgn from a
> > > UnivAlgn. Why would you want a SimpleAlgn you may ask. well, because
> > > UnivAlgn seems limited in the number of output formats possible (only
> > > fasta and raw, neither is optimal in printing alignments for visual
> > > inspection). This seems to still be true in 0.7. also, AlignIO only
> > > takes SimpleAlgn (is that a bug or a 'feature'?).
> > >
> > > so I suppose the questions are
> > > 1- how do you get a SimpleAln from UnivAln (short of saving UnivAln to a
> > > file in fasta format and reading it back again in SimpleAln, which by
> > > the way does not seems to work smoothly?
> > > 2- how do you pretty print a UnivAlgn (say clustalw format)?
> > >
> > > thanks for the help.
> > 
> > Unfortunately there currently is no straightforward way to convert between
> > SimpleAlign and UnivAln objects.  This is neither a "feature" nor a bug.
> > Rather an unfortunate historical consequence of the fact that the two
> > modules were developed independently.
> > 
> > In developing AlignIO.pm, I chose to use SimpleAlign for the alignment
> > objects because it was easier and met all of my needs at the time.  As I've
> > later needed a few features from UnivAln, I've added them to SimpleAlign
> > recently.  If you need some specific feature of UnivAln, let me know and if
> > it's not too complicated I'll see about adding it to the methods of
> > SimpleAlign.  As for converting all of UnivAln's capabilities to
> > SimpleAlign format, it's a bear I don't want to take on at this point, but
> > if some else wants to, that would be fine (then UnivAln could just
> > disappear).
> > 
> > In the interim, both UnivAln and SimpleAlign (via AlignIO) read and write
> > fasta formatted alignment files so you can always convert between the two
> > alignment objects that way (it's kludgy but it should work)
> > 
> > - Peter
> > 
> > _______________________________________________
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> 
> -- 
> Murad Nayal M.D. Ph.D.
> Department of Biochemistry and Molecular Biophysics
> College of Physicians and Surgeons of Columbia University
> 630 West 168th Street. New York, NY 10032
> Tel: 212-305-6884	Fax: 212-305-6926
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> 

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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
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