[Bioperl-l] change the location coordinates of a Bio::SeqFeatureI object

Peili Zhang peili at morgan.harvard.edu
Wed Jun 25 17:17:19 EDT 2003


I'm trying to do some coordinate translation for the locations of
SeqFeatures in a Bio::Seq object. my plan to achieve this is to first
flush out all seq features of the Bio::Seq object, and then add back the
array of features with the new coordinates.

for the features with simple locations (ie start..end), I can use
$feature->start($new_start) and $feature->end($new_end) to set the
locations to new coordinates, but how can I make such changes for the
seq features which have split locations? for instance, an mRNA feature
has a join location like join(10..20, 30..40, 50..60), its location will
be a Bio::Location::SplitLocationI object. I can retrieve the
sub-locations through the sub_Location() method. I need to mutate the
location of this mRNA feature  to be join(1010..1020, 1030..1040,
1050..1060). how do I do this?

thanks in advance for your help.


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