[Bioperl-l] Cannot guess alphabet error
jason.stajich at duke.edu
Thu Sep 22 22:28:24 EDT 2005
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:
> 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', -
> ------------- EXCEPTION -------------
> MSG: Got a sequence with no letters in it cannot guess alphabet 
> STACK Bio::PrimarySeq::_guess_alphabet /usr/lib/perl5/site_perl/
> STACK Bio::PrimarySeq::seq /usr/lib/perl5/site_perl/5.8.5/Bio/
> 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
> Wes Barris
> E-Mail: Wes.Barris at csiro.au
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
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