NAME

       Bio::SeqIO::metafasta - metafasta sequence input/output stream

SYNOPSIS

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

         use Bio::SeqIO;

         # read the metafasta file
         $io = Bio::SeqIO->new(-file => "test.metafasta",
                               -format => "metafasta" );

         $seq = $io->next_seq;

DESCRIPTION

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

       For sequence part the code is an exact copy of Bio::SeqIO::fasta module. The only added
       bits deal with meta data IO.

       The format of a metafasta file is

         >test
         ABCDEFHIJKLMNOPQRSTUVWXYZ
         &charge
         NBNAANCNJCNNNONNCNNUNNXNZ
         &chemical
         LBSAARCLJCLSMOIMCHHULRXRZ

       where the sequence block is followed by one or several meta blocks.  Each meta block
       starts with the ampersand character '&' in the first column and is immediately followed by
       the name of the meta data which continues until the new line. The meta data follows it.
       All characters, except new line, are important in meta data.

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://redmine.open-bio.org/projects/bioperl/

AUTHOR - Heikki Lehvaslaiho

       Email heikki-at-bioperl-dot-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
        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 to n Bio::PrimarySeqI objects

   width
        Title   : width
        Usage   : $obj->width($newval)
        Function: Get/Set the line width for METAFASTA output
        Returns : value of width
        Args    : newvalue (optional)