/ 
BioPerl-1.007001
River stage two • 60 direct dependents • 65 total dependents
/ Bio::SeqIO::raw

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 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

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 objects

write_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 object

variant

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