NAME
Bio::SeqIO::raw - raw sequence file input/output stream
SYNOPSIS
Do not use this module directly. Use it via the Bio::SeqIO class.
DESCRIPTION
This object can transform Bio::Seq objects to and from raw flat file databases.
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 listsSupport
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/AUTHORS
Ewan Birney E<lt>birney@ebi.ac.ukE<gt>
Lincoln Stein E<lt>lstein@cshl.orgE<gt>CONTRIBUTORS
Jason Stajich E<lt>jason@bioperl.org<gt>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 : $seq = $stream->next_seq()
Function: returns the next sequence in the stream
Returns : Bio::Seq object
Args :write_seq
Title : write_seq
Usage : $stream->write_seq($seq)
Function: writes the $seq object into the stream
Returns : 1 for success and 0 for error
Args : Array of Bio::PrimarySeqI objectswrite_qual
Title : write_qual
Usage : $stream->write_qual($seq)
Function: writes the $seq object into the stream
Returns : 1 for success and 0 for error
Args : Bio::Seq::Quality objectvariant
Title : variant
Usage : $format = $obj->variant();
Function: Get and set method for the sequence variant. For raw sequence, this
indicates whether to treat the input as multiple sequences (the
default) or as a single sequence.
Current values accepted are:
'single' single sequence
'multiple' multiple sequences (default)
Returns : string
Args : new value, string