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Bio::FeatureIO::gff(3)User Contributed Perl DocumentatioBio::FeatureIO::gff(3)

NAME
       Bio::FeatureIO::gff - read/write	GFF feature files

SYNOPSIS
	 my $feature; #get a Bio::SeqFeature::Annotated	somehow
	 my $featureOut	= Bio::FeatureIO->new(
	   -format => 'gff',
	   -version => 3,
	   -fh => \*STDOUT,
	   -validate_terms => 1, #boolean. validate ontology terms online?  default 0 (false).
	 );
	 $featureOut->write_feature($feature);

DESCRIPTION
	Currently implemented:

	version		read?	write?
	------------------------------
	GFF 1		  N	  N
	GFF 2		  N	  N
	GFF 2.5	(GTF)	  N	  Y
	GFF 3		  Y	  Y

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 the
       Bioperl mailing list.  Your participation is much appreciated.

	 bioperl-l@bioperl.org		       - General discussion
	 http://bioperl.org/wiki/Mailing_list  - 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 of
       the bugs	and their resolution. Bug reports can be submitted via the
       web:

	 http://bugzilla.open-bio.org/

AUTHOR
	Allen Day, <allenday@ucla.edu>

CONTRIBUTORS
	Steffen	Grossmann, <grossman@molgen.mpg.de>
	Scott Cain, <cain@cshl.edu>
	Rob Edwards <rob@salmonella.org>

APPENDIX
       The rest	of the documentation details each of the object	methods.
       Internal	methods	are usually preceded with a _

   next_feature()
	Usage	: my $feature =	$featureio->next_feature();
	Function: reads	a feature record from a	GFF stream and returns it as an	object.
	Returns	: a Bio::SeqFeature::Annotated object
	Args	: N/A

   next_feature_group
	Title	: next_feature_group
	Usage	: @feature_group = $stream->next_feature_group
	Function: Reads	the next feature_group from $stream and	returns	it.

		  Feature groups in GFF3 files are separated by	'###' directives. The
		  features in a	group might form a hierarchical	structure. The
		  complete hierarchy of	features is returned, i.e. the returned	array
		  represents only the top-level	features.  Lower-level features	can
		  be accessed using the	'get_SeqFeatures' method recursively.

	Example	: # getting the	complete hierarchy of features in a GFF3 file
		  my @toplevel_features;
		  while	(my @fg	= $stream->next_feature_group) {
		      push(@toplevel_features, @fg);
		  }
	Returns	: an array of Bio::SeqFeature::Annotated objects
	Args	: none

   next_seq()
       access the FASTA	section	(if any) at the	end of the GFF stream.	note
       that this method	will return undef if not all features in the stream
       have been handled

   write_feature()
	Usage	: $featureio->write_feature( Bio::SeqFeature::Annotated->new(...) );
	Function: writes a feature in GFF format.  the GFF version used	is governed by the
		  '-version' argument passed to	Bio::FeatureIO->new(), and defaults to GFF
		  version 3.
	Returns	: ###FIXME
	Args	: a Bio::SeqFeature::Annotated object.

ACCESSORS
   fasta_mode()
	Usage	: $obj->fasta_mode($newval)
	Function:
	Example	:
	Returns	: value	of fasta_mode (a scalar)
	Args	: on set, new value (a scalar or undef,	optional)

       Side effect when	setting: rewind	the file handle	a little bit to	get
       the last	carriage return	that was swallowed when	the previous line was
       processed.

   seqio()
	Usage	: $obj->seqio($newval)
	Function: holds	a Bio::SeqIO instance for handling the GFF3 ##FASTA section.
	Returns	: value	of seqio (a scalar)
	Args	: on set, new value (a scalar or undef,	optional)

   sequence_region()
	Usage	:
	Function: ###FIXME
	Returns	:
	Args	:

   so()
	Usage	: $obj->so($newval)
	Function: holds	a Sequence Ontology instance
	Returns	: value	of so (a scalar)
	Args	: on set, new value (a scalar or undef,	optional)

   validate()
	Usage	: $obj->validate($newval)
	Function: true if encountered ontology terms in	next_feature()
		  mode should be validated.
	Returns	: value	of validate (a scalar)
	Args	: on set, new value (a scalar or undef,	optional)

   version()
	Usage	: $obj->version($newval)
	Function: version of GFF to read/write.	 valid values are 1, 2,	2.5, and 3.
	Returns	: value	of version (a scalar)
	Args	: on set, new value (a scalar or undef,	optional)

INTERNAL METHODS
   _buffer_feature()
	Usage	:
	Function: ###FIXME
	Returns	:
	Args	:

_handle_directive()
       this method is called for lines beginning with '##'.

_handle_feature()
       this method is called for each line not beginning with '#'.  it parses
       the line	and returns a Bio::SeqFeature::Annotated object.

   _handle_non_reserved_tag()
	Usage	: $self->_handle_non_reserved_tag($feature,$tag,$value)
	Function: Deal with non-reserved word tags in the ninth	column
	Returns	: An updated Bio::SeqFeature::Annotated	object
	Args	: A Bio::SeqFeature::Annotated and a tag/value pair

       Note that this method can be overridden in a subclass to	provide
       special handling	of non-reserved	word tags.

   organism
       Gets/sets the organims from the organism	directive

_write_feature_1()
       write a feature in GFF v1 format.  currently not	implemented.

_write_feature_2()
       write a feature in GFF v2 format.  currently not	implemented.

_write_feature_25()
       write a feature in GFF v2.5 (aka	GTF) format.

_write_feature_3()
       write a feature in GFF v3 format.

perl v5.32.0			  2014-09-05		Bio::FeatureIO::gff(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR | CONTRIBUTORS | APPENDIX | ACCESSORS | INTERNAL METHODS

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