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

Brian Osborne brian_osborne at cognia.com
Mon Oct 25 21:58:23 EDT 2004


I've committed a change to qual.pm in bioperl-live that seems to fix this
(and a test for the fix in t/primaryqual.t), take a look.

Brian O.

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Carlos Mauricio
La Rota
Sent: Tuesday, October 19, 2004 11:09 AM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] problems with bioperl's Bio::SeqIO::qual

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

Bioperl-l mailing list
Bioperl-l at portal.open-bio.org

More information about the Bioperl-l mailing list