[Bioperl-l] Cannot guess alphabet error

[Wes Barris]

Jason Stajich wrote:

> 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.

Actually, I am.  In order to make the sample code a simple as possible,
I changed it to PrimarySeq.  This code also produces the error:

#!/usr/bin/perl -w
use strict;
use Bio::LocatableSeq;
my $myseq = new Bio::LocatableSeq(-seq=>'AGCT', -id=>'myseq', -alphabet=>'dna');
$myseq->alphabet('dna');
$myseq->seq('----');



> 
> 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
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at portal.open-bio.org
>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>
> 
> -- 
> Jason Stajich
> Duke University
> http://www.duke.edu/~jes12
> 


-- 
Wes Barris
E-Mail: Wes.Barris at csiro.au