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.

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/MailList.shtml - About the mailing lists

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 email or the web: bioperl-bugs@bioperl.org http://bugzilla.bioperl.org/ Email dblock@gene.pbi.nrc.ca Ewan Birney forced me to this... 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