Provided by: libbio-perl-perl_1.7.2-2_all bug


       Bio::SeqIO::fasta - fasta sequence 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 fasta flat file databases.


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AUTHORS - Ewan Birney & Lincoln Stein



       Jason Stajich,


       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, or nothing if no more available
        Args    : NONE

        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 1 or more Bio::PrimarySeqI objects

        Title   : width
        Usage   : $obj->width($newval)
        Function: Get/Set the line width for FASTA output (not counting whitespace).
        Returns : value of width
        Args    : newvalue (optional)

        Title   : block
        Usage   : $obj->block($newval)
        Function: Get/Set the length of each block for FASTA output. Sequence blocks
                  will be split with a space. Configuring block, to a value of 10 for
                  example, allows one to easily identify a position in a sequence by eye.
        Default : same value used for width.
        Returns : value of block
        Args    : newvalue (optional)

        Title   : preferred_id_type
        Usage   : $obj->preferred_id_type('accession')
        Function: Get/Set the preferred type of identifier to use in the ">ID" position
                  for FASTA output.
        Returns : string, one of values defined in @Bio::SeqIO::fasta::SEQ_ID_TYPES.
        Default : display
        Args    : string when setting. This must be one of values defined in
                  @Bio::SeqIO::fasta::SEQ_ID_TYPES. Allowable values:
                  accession, accession.version, display, primary
        Throws  : fatal exception if the supplied id type is not in @SEQ_ID_TYPES.