[Bioperl-l] Locatable sequence with numbers

[Iain Wallace]

Hi 

I am trying to create a file for clustalw that is of that includes the
secondary structure mask

!GM_id 1111144444411
id     GVPINVSCTGSPQ

My problem is that the code below doesn't work as $gap_mask is a string
of numbers, and not a proper sequence.

 my $newseq1 = new Bio::LocatableSeq(-seq => $gap_mask,
                                        -id => "!GM_".$seq->id,
                                        -start => 1,
                                        -end => $seq->length());
        print "adding id:\t",$seq->id,"\n";
        $Align->add_seq($newseq1);

The error that gets generated is 
 
-------------------- WARNING ---------------------
MSG: seq doesn't validate, mismatch is 1
---------------------------------------------------
 
------------- EXCEPTION  -------------
MSG: Attempting to set the sequence to
[12211111114444444444412222222112222221] which does not look healthy
STACK Bio::PrimarySeq::seq
/usr/lib/perl5/site_perl/5.8.0/Bio/PrimarySeq.pm:268
STACK Bio::PrimarySeq::new
/usr/lib/perl5/site_perl/5.8.0/Bio/PrimarySeq.pm:217
STACK Bio::LocatableSeq::new
/usr/lib/perl5/site_perl/5.8.0/Bio/LocatableSeq.pm:100
STACK toplevel ./dssp.pl:61
 
--------------------------------------


Does anyone know how I could get around this ? 

Thanks 

Iain