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)