Bio::SeqIO::metafasta.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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:
   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_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)