- AUTHOR Chad Matsalla
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).
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.
email@example.com - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Please direct usage questions or support issues to the mailing list:
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.
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:
AUTHOR Chad Matsalla
Chad Matsalla firstname.lastname@example.org
Jason Stajich, email@example.com
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.