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)