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Bio::SeqIO::metafasta(User Contributed Perl DocumentatBio::SeqIO::metafasta(3)

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)

perl v5.32.1			  2019-12-07	      Bio::SeqIO::metafasta(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Heikki Lehvaslaiho | APPENDIX

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