Bio::SeqIO::qual(3pm)					User Contributed Perl Documentation				     Bio::SeqIO::qual(3pm)

NAME

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

SYNOPSIS

       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);

DESCRIPTION

       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).

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one
       of the Bioperl mailing lists.  Your participation is much appreciated.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
       it. Please include a thorough description of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution.  Bug reports can be submitted via the
       web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR Chad Matsalla
       Chad Matsalla bioinformatics@dieselwurks.com

CONTRIBUTORS

       Jason Stajich, jason@bioperl.org

APPENDIX

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

   next_seq()
	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.

   _next_qual
	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.

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

   width
	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)

   write_seq
	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.

perl v5.14.2							    2012-03-02						     Bio::SeqIO::qual(3pm)