Provided by: libbio-perl-perl_1.6.923-1_all bug


       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

         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.