[Bioperl-l] Bio::Seq::Quality description line problem

David Messina dmessina at wustl.edu
Fri May 5 10:53:15 EDT 2006


T.D.,

 From a cursory walk through your code in a debugger, it looks like  
Bio::SeqIO::qual's write_seq method doesn't read the 'desc' out of  
the Bio::Seq::Quality object.

I think there should be something like this:
if ($source->can('desc') and my $desc = $source->desc()) {
     $desc =~ s/\n//g;
}
$header .= " $desc";

before line 218 in Bio::SeqIO::qual (where the header is printed):
$self->_print (">$header \n");

Dave



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