[Bioperl-l] problems with bioperl's Bio::SeqIO::qual

Carlos Mauricio La Rota cmlarota at vbi.vt.edu
Tue Oct 19 11:09:02 EDT 2004

Hello friends (and Chad Matsalla)

I am having problems with the method (function)  "write_seq()"   
implemented in  Bio::SeqIO::qual .

I have an output stream:    __  $QualOUT  = Bio::SeqIO->new(-fh => 
\*QUALOUT, '-format' =>'qual');  __   that I am trying to print into 
with preformed PrimaryQual objects.  These objects have been loaded 
with Id(),  quality values, and a description  (the rest of the fasta 
sequence header that is not part of its id).

However,  the method that writes the object to the OUT stream does not 
care to print the description if there is one available.

So I tried instead to manually override the id in the $source object by 
giving it a header description when printing like this:

print $QualOUT->write_seq(-source => $outQualObj ,  -header => 

where $SeqHeader  had been predefined as the concatenation of the id 
and the description (basically a string).   However,   method 
write_seq()  continues to use the objects id,  even though I am telling 
it to use my text defined in the "-header" flag.

I basically want to print out a quality file that contain the exact 
same headers as the corresponding fasta file  (which is the way Phred 
prints them).


C.Mauricio La Rota
Lawrence Lab
Virginia Bioinformatics Institute

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