/ 
BioPerl-1.7.8
River stage two • 60 direct dependents • 65 total dependents
/ Bio::SeqIO::qual

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.