Bio::SeqIO::raw - raw sequence file input/output stream


Do not use this module directly. Use it via the Bio::SeqIO class.


This object can transform Bio::Seq objects to and from raw flat file databases.


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Please direct usage questions or support issues to the mailing list:

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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:


  Ewan Birney   E<lt><gt>
  Lincoln Stein E<lt>lstein@cshl.orgE<gt>


  Jason Stajich E<lt><gt>


The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _


 Title   : next_seq
 Usage   : $seq = $stream->next_seq()
 Function: returns the next sequence in the stream
 Returns : Bio::Seq object
 Args    :


 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


 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


 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