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://github.com/bioperl/bioperl-live/issues

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)