[Bioperl-l] Translation Question

Raymond Auerbach Raymond.Auerbach at NAU.EDU
Mon Oct 11 19:39:15 EDT 2004

I am new to Bioperl and was wondering what is wrong with the following code:



use strict;

use Bio::Perl;


my $seq_obj = new_sequence("--acg-uuu","test","A1234");


print translate_as_string($seq_obj);




I expect to see XXF returned, but instead I get an exception:


------------- EXCEPTION  -------------

MSG: Can't translate an amino acid sequence.

STACK Bio::PrimarySeqI::translate C:/Perl/site/lib/Bio/PrimarySeqI.pm:527

STACK Bio::Perl::translate C:/Perl/site/lib/Bio/Perl.pm:559

STACK Bio::Perl::translate_as_string C:/Perl/site/lib/Bio/Perl.pm:580

STACK toplevel test2.pl:12




Any ideas?  I need to be able to do a translation with gaps since a sequence
alignment script feeds into this.  Thanks!


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