| Bio::SeqIO::metafasta(3pm) | User Contributed Perl Documentation | Bio::SeqIO::metafasta(3pm) |
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.
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
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.
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
Email heikki-at-bioperl-dot-org
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)
| 2020-10-28 | perl v5.30.3 |