Manual Reference Pages - BIO::SEQIO::METAFASTA (3)
Bio::SeqIO::metafasta - metafasta sequence input/output stream
Do not use this module directly. Use it via the Bio::SeqIO class.
# read the metafasta file
$io = Bio::SeqIO->new(-file => "test.metafasta",
-format => "metafasta" );
$seq = $io->next_seq;
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
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.
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AUTHOR - Heikki Lehvaslaiho
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
Title : next_seq
Usage : $seq = $stream->next_seq()
Function: returns the next sequence in the stream
Returns : Bio::Seq object
Args : NONE
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
Title : width
Usage : $obj->width($newval)
Function: Get/Set the line width for METAFASTA output
Returns : value of width
Args : newvalue (optional)
|perl v5.20.3 ||BIO::SEQIO::METAFASTA (3) ||2016-04-05 |
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