[Bioperl-l] add_seq method

luisa pugliese luisa.pugliese at safan-bioinformatics.it
Tue May 18 06:47:01 EDT 2004

Hi bioperlers,
   I am trying to use the addseq method of SimpleAlign and I get always an error message.
Here is the script I used:
#!/usr/bin/perl -w
use strict;

use Bio::PrimarySeq;
use Bio::AlignIO;
use Bio::SimpleAlign;

my $seq_stru=new Bio::PrimarySeq(-seq =>'AGTYHILMKPTRED',
                                                     -id => 'seq_stru');
my $in = Bio::AlignIO->new(-format => 'clustalw',
                                        -file   => '1433-fam.aln');
my $aln = $in->next_aln;

and the error message is:

------------- EXCEPTION  -------------
MSG: Unable to process non locatable sequences [Bio::PrimarySeq]
STACK Bio::SimpleAlign::add_seq /home/luisa/bioperl_new/bioperl-1.4/Bio/SimpleAlign.pm:250
STACK toplevel test.pl:17

Does anybody know what I am doing wrong and what the error message means?
Do you know if it is possible to use add_seq method adding  protein sequence with the aminoacids in the 3 letter code?

Thank you and best regards


Luisa Pugliese, Ph.D.
luisa.pugliese at safan-bioinformatics.it
Corso Tazzoli 215/13 -10137 Torino - ITALY
tel +39 011 3026230
cell. +39 333 6130644

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