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Bio::UpdateableSeqI(3)User Contributed Perl DocumentatioBio::UpdateableSeqI(3)

       Bio::UpdateableSeqI - Descendant	of Bio::SeqI that allows updates

       See Bio::SeqI for most of the documentation.  See the documentation of
       the methods for further details.

       Bio::UpdateableSeqI is an interface for Sequence	objects	which are
       expected	to allow users to perform basic	editing	functions
       (update/delete) on their	component SeqFeatures.

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       rather than to the module maintainer directly. Many experienced and
       reponsive experts will be able look at the problem and quickly address
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       Report bugs to the Bioperl bug tracking system to help us keep track of
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AUTHOR - David Block

       Ewan Birney forced me to	this...

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

	Title	: delete_feature
	Usage	: my $orphanlist=$self->delete_feature($feature,$transcript,$gene);
	Function: deletes the specified	$feature from the given	transcript, if $transcript is sent and exists and $feature is a	feature	of $transcript,
		  or from $gene	if the $feature	is a feature of	$gene, or from $self if	$transcript and	$gene are not sent.  Keeps track of the	features
		  of the $gene object that may be left as orphans and returns them as a	listref.
	Example	: I want to delete transcript 'abc' of gene 'def', with	three exons, leaving only transcript 'ghi' with	two exons.
		  This will leave exons	1 and 3	part of	'ghi', but exon	2 will become an orphan.
		  my $orphanlist=$seq->delete_feature($transcript{'abc'},undef,$gene{'def'});
		  $orphanlist is a reference to	a list containing $exon{'2'};
	Returns	: a listref of orphaned	features after the deletion of $feature	(optional)
	Args	: $feature - the feature to be deleted
		  $transcript -	the transcript containing the $feature,	so that	a $feature can be removed from only one	transcript when	there are multiple
				transcripts in a gene.
		  $gene	- the gene containing the $transcript and/or the $feature

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


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