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

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

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

DESCRIPTION
       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.

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_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 - David Block
       Email dblock@gene.pbi.nrc.ca

CONTRIBUTORS
       Ewan Birney forced me to	this...

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

   delete_feature
	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)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - David Block | CONTRIBUTORS | APPENDIX

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