- AUTHOR - Heikki Lehvaslaiho
Bio::SeqIO::metafasta - metafasta sequence input/output stream
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;
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.
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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)