[Bioperl-l] Translation Question

[Raymond Auerbach]

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!

-Ray