[Bioperl-l] Locatable sequence with numbers

Iain Wallace iain.wallace at ucd.ie
Mon Mar 8 11:57:34 EST 2004


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

!GM_id 1111144444411

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";

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
STACK Bio::PrimarySeq::new
STACK Bio::LocatableSeq::new
STACK toplevel ./dssp.pl:61

Does anyone know how I could get around this ? 



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