[Bioperl-l] printing UnivAlgn

Murad Nayal murad@godel.bioc.columbia.edu
Fri, 15 Dec 2000 14:14:16 +0100


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.

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