Bio::UpdateableSeqI(3) 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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AUTHOR - David Block

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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