- 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).
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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.