Bio::SeqIO::metafasta(3pm) User Contributed Perl Documentation 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://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 : 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)
perl v5.14.2 2012-03-02 Bio::SeqIO::metafasta(3pm)