[Bioperl-l] printing UnivAlgn

Murad Nayal murad@godel.bioc.columbia.edu
Fri, 15 Dec 2000 21:07:19 +0100

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. 

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