/ 
FAST-1.06
River stage zero No dependents
/ FAST::Bio::SeqIO::metafasta

NAME

FAST::Bio::SeqIO::metafasta - metafasta sequence input/output stream

SYNOPSIS

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

use FAST::Bio::SeqIO;

# read the metafasta file
$io = FAST::Bio::SeqIO->new(-file => "test.metafasta",
                      -format => "metafasta" );

$seq = $io->next_seq;

DESCRIPTION

This object can transform FAST::Bio::Seq::Meta objects to and from metafasta flat file databases.

For sequence part the code is an exact copy of FAST::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 : FAST::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 FAST::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)