Bio::UpdateableSeqI man page on Fedora

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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:

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

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 v5.14.1			  2011-07-22		Bio::UpdateableSeqI(3)
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