Ewan Birney

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).

DESCRIPTION

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

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://www.bioperl.org/MailList.shtml  - About the mailing lists

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 email or the web:

  bioperl-bugs@bio.perl.org
  http://bio.perl.org/bioperl-bugs/

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

write_seq

 Title   : write_seq(-source => $source, -header => "some information")
 Usage   : $obj->write_seq(     -source => $source,
                                -header => "some information");
 Function: Write out an list of quality values to a fasta-style file.
 Returns : Nothing.
 Args    : Requires: a reference to a SeqWithQuality object or a
        PrimaryQual object as the -source. Optional: information
        for the header.
 Notes   : If no -header is provided, $obj->id() will be used where
        $obj is a reference to either a SeqWithQuality object or a
        PrimaryQual object. If $source->id() fails, ">unknown" will be
        the header. If the SeqWithQuality object has $source->length() of
        "DIFFERENT" (read the pod, luke), write_qual will use the length
        of the PrimaryQual object within the SeqWithQuality object.