[Bioperl-l] Cannot guess alphabet error

[Jason Stajich]

use Bio::LocatableSeq for building alignments - these can be '---'  
seqs.  You'll see these are required when adding sequences to a  
BIo::SimpleAlign object for writing out to msf.

On Sep 22, 2005, at 10:14 PM, Wes Barris wrote:

> Hi,
>
> The following code produces the error shown.  What is the correct way
> to set the alphabet of a primary (or locatable) seq?
>
> #!/usr/bin/perl -w
> use strict;
> use Bio::PrimarySeq;
> my $myseq = new Bio::PrimarySeq(-seq=>'AGCT', -id=>'myseq', - 
> alphabet=>'dna');
> $myseq->alphabet('dna');
> $myseq->seq('----');
>
>
> ------------- EXCEPTION  -------------
> MSG: Got a sequence with no letters in it cannot guess alphabet []
> STACK Bio::PrimarySeq::_guess_alphabet /usr/lib/perl5/site_perl/ 
> 5.8.5/Bio/PrimarySeq.pm:837
> STACK Bio::PrimarySeq::seq /usr/lib/perl5/site_perl/5.8.5/Bio/ 
> PrimarySeq.pm:279
> STACK toplevel /home/wes/soft/ace/test.pl:6
>
> It might seem to be a silly thing to want to do (setting a  
> sequences to
> a series of dashes).  My reason for wanting to do this is involves the
> creation of an alighment (msf) file.
>
> I am using a fresh version of bioperl-live, perl 5.8.5, Linux RHEL  
> 4.1.
> -- 
> Wes Barris
> E-Mail: Wes.Barris at csiro.au
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>

--
Jason Stajich
Duke University
http://www.duke.edu/~jes12