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://github.com/bioperl/bioperl-live/issues
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.