NAME

       Bio::SeqIO::fasta - fasta sequence 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 fasta 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 & Lincoln Stein

       Email: birney@ebi.ac.uk
              lstein@cshl.org

CONTRIBUTORS

       Jason Stajich, jason-at-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   : $seq = $stream->next_seq()
        Function: returns the next sequence in the stream
        Returns : Bio::Seq object, or nothing if no more available
        Args    : NONE

   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 1 or more Bio::PrimarySeqI objects

   width
        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)

   block
        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 to easily indentify a position in a sequence by eye.
        Default : same value used for width.
        Returns : value of block
        Args    : newvalue (optional)

   preferred_id_type
        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.