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Bio::SeqIO::game::featUserlContributed Perl DoBio::SeqIO::game::featHandler(3)

NAME
       Bio::SeqIO::game::featHandler --	a class	for handling feature elements

SYNOPSIS
       This module is not used directly

DESCRIPTION
       Bio::SeqIO::game::featHandler converts game XML <annotation> elements
       into flattened Bio::SeqFeature::Generic objects to be added to the
       sequence

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 of
       the bugs	and their resolution. Bug reports can be submitted via the
       web:

	 https://github.com/bioperl/bioperl-live/issues

AUTHOR - Sheldon McKay
       Email mckays@cshl.edu

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

   new
	Title	: new
	Usage	: my $featHandler = Bio::SeqIO::game::featHandler->new($seq, $seq_h, $ann_l)
	Function: creates an object to deal with sequence features
	Returns	: a handler object
	Args	: $seq	 -- a Bio::SeqI	compliant object
		  $seq_h -- ref. to a hash of other sequences associated
			    with the main sequence (proteins, etc)
		  $ann_l -- ref. to a list of annotations

   add_source
	Title	: add_source
	Usage	: $featHandler->add_source($seq->length, \%tags);
	Function: creates a source feature
	Returns	: a Bio::SeqFeature::Generic object
	Args	: sequence length and a	ref. to	a hash of tag/value attributes

   has_gene
	Title	: has_gene
	Usage	: my $gene = $self->_has_gene($gene, $gname, $id)
	Function: method to get/set the	current	gene feature
	Returns	: a Bio::SeqFeature::Generic object (if	there is a gene)
	Args	: (optional)
		  $gene	 -- an XML element for the annotation
		  $gname -- gene name
		  $id	 -- gene ID (not always	the same as the	name)

   _has_CDS
	Title	: _has_CDS
	Usage	: my $cds = $self->_has_CDS
	Function: internal getter/setter for CDS features
	Returns	: a Bio::SeqFeature::Generic transcript	object (or nothing)
	Args	: a Bio::SeqFeature::Generic transcript	feature

   add_annotation
	Title	: add_annotation
	Usage	: $featHandler->add_annotation($seq, $type, $id, $tags,	$feats)
	Function: converts a containment hierarchy into	an ordered list	of flat	features
	Returns	: nothing
	Args	: $seq	 -- a Bio::SeqI	compliant object
		  $type	 -- the	annotation type
		  $id	 -- the	anotation ID
		  $tags	 -- ref. to a hash of tag/value	attributes
		  $feats -- ref	to an array of Bio::SeqFeature::Generic	objects

   _add_generic_annotation
	Title	: _add_generic_annotation
	Usage	: $self->_add_generic_annotation($seq, $type, $id, $tags, $feats)
	Function: an internal method to	handle non-gene	annotations
	Returns	: nothing
	Args	: $seq	 -- a Bio::SeqI	compliant object
		  $type	 -- the	annotation type
		  $id	 -- the	anotation ID
		  $tags	 -- ref. to a hash of tag/value	attributes
		  $feats -- ref	to an array of Bio::SeqFeature::Generic	objects

   feature_set
	Title	: feature_set
	Usage	: push @feats, $featHandler->feature_set($id, $gname, $set, $anntype);
	Function: handles <feature_span> hierarchies (usually a	transcript)
	Returns	: a list of Bio::SeqFeature::Generic objects
	Args	: $id	   -- ID of the	feature	set
		  $gname   -- name of the gene
		  $set	   -- the <feature_set>	object
		  $anntype -- type of the parent annotation

   _build_feature_set
	Title	: _build_feature_set
	Usage	: $self->_build_feature_set($set, 1) # 1 flag means retain the exon as a subfeat
	Function: an internal method to	process	attributes and subfeats	of a feature set
	Returns	: nothing
	Args	: $set -- a <feature_set> element
		  1    -- optional flag	to retain exons	as subfeats.  Otherwise, they will
			  be converted to sublocations of a parent CDS feature

   _add_feature_span
	Title	: _add_feature_span
	Usage	: $self->_add_feature_span($el,	1)
	Function: an internal method to	process	<feature_span> elements
	Returns	: nothing
	Args	: $el -- a <feature_span> element
		  1   -- an optional flag to retain exons as subfeatures

   _add_CDS
	Title	: _add_CDS
	Usage	: my $cds = $self->_add_CDS($transcript, $tags)
	Function: an internal method to	create a CDS feature from a transcript feature
	Returns	: a Bio::SeqFeature::Generic object
	Args	: $transcript -- a Bio::SeqFeature::Generic object for a transcript
		  $tags	      -- ref. to a hash	of tag/value attributes

perl v5.24.1			  2017-07-08  Bio::SeqIO::game::featHandler(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Sheldon McKay | APPENDIX

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