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Bio::SeqIO::qual - .qual file input/output stream


Do not use this module directly. Use it via the Bio::SeqIO class (see Bio::SeqIO for details).

  my $in_qual = Bio::SeqIO->new(-file    => $qualfile,
                                -format  => 'qual',
                                -width   => $width,
                                -verbose => $verbose);


This object can transform .qual (similar to fasta) objects to and from Bio::Seq::Quality objects. See Bio::Seq::Quality for details.

Like the fasta module, it can take an argument '-width' to change the number of values per line (defaults to 50).


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AUTHOR Chad Matsalla

Chad Matsalla


Jason Stajich,


The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _


 Title   : next_seq()
 Usage   : $scf = $stream->next_seq()
 Function: returns the next scf sequence in the stream
 Returns : Bio::Seq::PrimaryQual object
 Notes   : Get the next quality sequence from the stream.


 Title   : _next_qual
 Usage   : $seq = $stream->_next_qual() (but do not do
          that. Use $stream->next_seq() instead)
 Function: returns the next quality in the stream
 Returns : Bio::Seq::PrimaryQual object
 Args    : NONE
 Notes  : An internal method. Gets the next quality in
                the stream.


 Title   : next_primary_qual()
 Usage   : $seq = $stream->next_primary_qual()
 Function: returns the next sequence in the stream
 Returns : Bio::PrimaryQual object
 Args    : NONE


 Title   : width
 Usage   : $obj->width($newval)
 Function: Get/Set the number of values per line  for FASTA-like output
 Returns : value of width
 Args    : newvalue (optional)


 Title   : write_seq
 Usage   : $obj->write_seq( -source => $source,
                            -header  => "some information"
                            -oneline => 0);
 Function: Write out a list of quality values to a fasta-style file.
 Returns : Nothing.
 Args    : Requires a reference to a Bio::Seq::Quality object or a
           PrimaryQual object as the -source. Option 1: information
           for the header. Option 2: whether the quality score should
           be on a single line or not
 Notes   : If no -header is provided, $obj->id() will be used where
           $obj is a reference to either a Quality object or a
           PrimaryQual object. If $source->id() fails, "unknown" will
           be the header. If the Quality object has $source->length()
           of "DIFFERENT" (read the pod, luke), write_seq will use the
           length of the PrimaryQual object within the Quality object.