[Bioperl-l] Cannot guess alphabet error
wes.barris at csiro.au
Thu Sep 22 22:35:02 EDT 2005
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:
my $myseq = new Bio::LocatableSeq(-seq=>'AGCT', -id=>'myseq', -alphabet=>'dna');
> 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 4.1.
>> Wes Barris
>> E-Mail: Wes.Barris at csiro.au
>> Bioperl-l mailing list
>> Bioperl-l at portal.open-bio.org
> Jason Stajich
> Duke University
E-Mail: Wes.Barris at csiro.au
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