Bio::AlignIO::metafasta(3)

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

  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:

  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)