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

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://bugzilla.bioperl.org/ Chad Matsalla bioinformatics@dieselwurks.com Jason Stajich, jason@bioperl.org 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_seq will use the length of the PrimaryQual object within the SeqWithQuality object.