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Bio::SeqIO::genbank(3)User Contributed Perl DocumentatioBio::SeqIO::genbank(3)

NAME
       Bio::SeqIO::genbank - GenBank sequence input/output stream

SYNOPSIS
       It is probably best not to use this object directly, but	rather go
       through the SeqIO handler:

	   $stream = Bio::SeqIO->new(-file   =>	$filename,
				     -format =>	'GenBank');

	   while ( my $seq = $stream->next_seq ) {
	       # do something with $seq
	   }

DESCRIPTION
       This object can transform Bio::Seq objects to and from GenBank flat
       file databases.

       There is	some flexibility here about how	to write GenBank output	that
       is not fully documented.

   Optional functions
       _show_dna()
	  (output only)	shows the dna or not

       _post_sort()
	  (output only)	provides a sorting func	which is applied to the
	  FTHelpers before printing

       _id_generation_func()
	  This is function which is called as

	     print "ID	 ", $func($seq), "\n";

	  To generate the ID line. If it is not	there, it generates a sensible
	  ID line using	a number of tools.

	  If you want to output	annotations in Genbank format they need	to be
	  stored in a Bio::Annotation::Collection object which is accessible
	  through the Bio::SeqI	interface method annotation().

	  The following	are the	names of the keys which	are pulled from	a
	  Bio::Annotation::Collection object:

	   reference	   - Should contain Bio::Annotation::Reference objects
	   comment	   - Should contain Bio::Annotation::Comment objects
	   dblink	   - Should contain a Bio::Annotation::DBLink object
	   segment	   - Should contain a Bio::Annotation::SimpleValue object
	   origin	   - Should contain a Bio::Annotation::SimpleValue object
	   wgs		   - Should contain a Bio::Annotation::SimpleValue object

Where does the data go?
       Data parsed in Bio::SeqIO::genbank is stored in a variety of data
       fields in the sequence object that is returned. Here is a partial list
       of fields.

       Items listed as RichSeq or Seq or PrimarySeq and	then NAME() tell you
       the top level object which defines a function called NAME() which
       stores this information.

       Items listed as Annotation 'NAME' tell you the data is stored the
       associated Bio::AnnotationCollectionI object which is associated	with
       Bio::Seq	objects.  If it	is explicitly requested	that no	annotations
       should be stored	when parsing a record of course	they will not be
       available when you try and get them.  If	you are	having this problem
       look at the type	of SeqBuilder that is being used to construct your
       sequence	object.

	Comments	     Annotation	'comment'
	References	     Annotation	'reference'
	Segment		     Annotation	'segment'
	Origin		     Annotation	'origin'
	Dbsource	     Annotation	'dblink'

	Accessions	     PrimarySeq	accession_number()
	Secondary accessions RichSeq get_secondary_accessions()
	GI number	     PrimarySeq	primary_id()
	LOCUS		     PrimarySeq	display_id()
	Keywords	     RichSeq get_keywords()
	Dates		     RichSeq get_dates()
	Molecule	     RichSeq molecule()
	Seq Version	     RichSeq seq_version()
	PID		     RichSeq pid()
	Division	     RichSeq division()
	Features	     Seq get_SeqFeatures()
	Alphabet	     PrimarySeq	alphabet()
	Definition	     PrimarySeq	description() or desc()
	Version		     PrimarySeq	version()

	Sequence	     PrimarySeq	seq()

       There is	more information in the	Feature-Annotation HOWTO about each
       field and how it	is mapped to the Sequence object
       <http://bioperl.org/howtos/Features_and_Annotations_HOWTO.html>.

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 - Bioperl Project
       bioperl-l at bioperl.org

       Original	author Elia Stupka, elia -at- tigem.it

CONTRIBUTORS
       Ewan Birney birney at ebi.ac.uk Jason Stajich jason at bioperl.org
       Chris Mungall cjm at fruitfly.bdgp.berkeley.edu Lincoln Stein lstein at
       cshl.org	Heikki Lehvaslaiho, heikki at ebi.ac.uk	Hilmar Lapp, hlapp at
       gmx.net Donald G. Jackson, donald.jackson at bms.com James Wasmuth,
       james.wasmuth at	ed.ac.uk Brian Osborne,	bosborne at alum.mit.edu Chris
       Fields, cjfields	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	:

   write_seq
	Title	: write_seq
	Usage	: $stream->write_seq($seq)
	Function: writes the $seq object (must be seq) to the stream
	Returns	: 1 for	success	and 0 for error
	Args	: array	of 1 to	n Bio::SeqI objects

   _print_GenBank_FTHelper
	Title	: _print_GenBank_FTHelper
	Usage	:
	Function:
	Example	:
	Returns	:
	Args	:

   _read_GenBank_References
	Title	: _read_GenBank_References
	Usage	:
	Function: Reads	references from	GenBank	format.	Internal function really
	Returns	:
	Args	:

   _add_ref_to_array
       Title: _add_ref_to_array	Usage: Function: Adds a	Reference object to an
       array of	Reference objects, takes
		 care of possible cleanups to be done (currently, only author
       and title
		 will be chopped of trailing semicolons).  Args:     A
       reference to an array of	Reference objects and
		 the Reference object to be added Returns: nothing

   _read_GenBank_Species
	Title	: _read_GenBank_Species
	Usage	:
	Function: Reads	the GenBank Organism species and classification
		  lines. Able to deal with unconvential	Organism naming
		  formats, and varietas	in plants
	Example	: ORGANISM  unknown marine gamma proteobacterium NOR5
		  $genus = undef
		  $species = unknown marine gamma proteobacterium NOR5

		  ORGANISM  Drosophila sp. 'white tip scutellum'
		  $genus = Drosophila
		  $species = sp. 'white	tip scutellum'
		  (yes,	this really is a species and that is its name)
		  $subspecies =	undef

		  ORGANISM  Ajellomyces	capsulatus var.	farciminosus
		  $genus = Ajellomyces
		  $species = capsulatus
		  $subspecies =	var. farciminosus

		  ORGANISM  Hepatitis delta virus
		  $genus = undef (though this virus has	a genus	in its lineage,	we
				  cannot know that without a database lookup)
		  $species = Hepatitis delta virus

	Returns	: A Bio::Species object
	Args	: A reference to the current line buffer

   _read_FTHelper_GenBank
	Title	: _read_FTHelper_GenBank
	Usage	: _read_FTHelper_GenBank($buffer)
	Function: reads	the next FT key	line
	Example	:
	Returns	: Bio::SeqIO::FTHelper object
	Args	: filehandle and reference to a	scalar

   _write_line_GenBank
	Title	: _write_line_GenBank
	Usage	:
	Function: internal function
	Example	:
	Returns	:
	Args	:

   _write_line_GenBank_regex
	Title	: _write_line_GenBank_regex
	Usage	:
	Function: internal function for	writing	lines of specified
		  length, with different first and the next line
		  left hand headers and	split at specific points in the
		  text
	Example	:
	Returns	: nothing
	Args	: file handle,
		  first	header,
		  second header,
		  text-line,
		  regex	for line breaks,
		  total	line length

   _post_sort
	Title	: _post_sort
	Usage	: $obj->_post_sort($newval)
	Function:
	Returns	: value	of _post_sort
	Args	: newvalue (optional)

   _show_dna
	Title	: _show_dna
	Usage	: $obj->_show_dna($newval)
	Function:
	Returns	: value	of _show_dna
	Args	: newvalue (optional)

   _id_generation_func
	Title	: _id_generation_func
	Usage	: $obj->_id_generation_func($newval)
	Function:
	Returns	: value	of _id_generation_func
	Args	: newvalue (optional)

   _ac_generation_func
	Title	: _ac_generation_func
	Usage	: $obj->_ac_generation_func($newval)
	Function:
	Returns	: value	of _ac_generation_func
	Args	: newvalue (optional)

   _sv_generation_func
	Title	: _sv_generation_func
	Usage	: $obj->_sv_generation_func($newval)
	Function:
	Returns	: value	of _sv_generation_func
	Args	: newvalue (optional)

   _kw_generation_func
	Title	: _kw_generation_func
	Usage	: $obj->_kw_generation_func($newval)
	Function:
	Returns	: value	of _kw_generation_func
	Args	: newvalue (optional)

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

NAME | SYNOPSIS | DESCRIPTION | Where does the data go? | FEEDBACK | AUTHOR - Bioperl Project | CONTRIBUTORS | APPENDIX

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