Bio::SeqIO::metafasta(3pm)				User Contributed Perl Documentation				Bio::SeqIO::metafasta(3pm)

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)

perl v5.14.2							    2012-03-02						Bio::SeqIO::metafasta(3pm)