NAME

Bio::AlignIO::metafasta - Metafasta MSA Sequence input/output stream

SYNOPSIS

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

DESCRIPTION

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

The format of a metafasta file is

>test/1-25
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.

SEE ALSO

Bio::SeqIO::metafasta

FEEDBACK

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:

http://bugzilla.open-bio.org/

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_aln

 Title   : next_aln
 Usage   : $aln = $stream->next_aln()
 Function: returns the next alignment in the stream.
 Returns : L<Bio::Align::AlignI> object - returns 0 on end of file
	    or on error
 Args    : NONE

write_aln

Title   : write_aln
Usage   : $stream->write_aln(@aln)
Function: writes the $aln object into the stream in fasta format
Returns : 1 for success and 0 for error
Args    : L<Bio::Align::AlignI> object

width

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