diff variant_effect_predictor/Bio/Graphics/Util.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Graphics/Util.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,40 @@
+package Bio::Graphics::Util;
+
+# $Id: Util.pm,v 1.2.2.2 2003/07/06 21:53:55 heikki Exp $
+# Non object-oriented utilities used here-and-there in Bio::Graphics modules
+
+use strict;
+require Exporter;
+use vars '@ISA','@EXPORT','@EXPORT_OK';
+@ISA = 'Exporter';
+@EXPORT = 'frame_and_offset';
+
+
+=over 4
+
+=item ($frame,$offset) = frame_and_offset($pos,$strand,$phase)
+
+Calculate the reading frame for a given genomic position, strand and
+phase.  The offset is the offset from $pos to the first nucleotide
+of the reading frame.
+
+In a scalar context, returns the frame only.
+
+=back
+
+=cut
+
+sub frame_and_offset {
+  my ($pos,$strand,$phase) = @_;
+  $strand ||= +1;
+  $phase  ||= 0;
+  my $frame = $strand >= 0 
+    ? ($pos - $phase - 1) % 3
+    : (1 - $pos - $phase) % 3;
+  my $offset = -$phase % 3;
+  $offset   *= -1 if $strand < 0;
+  return wantarray ? ($frame,$offset) : $frame;
+}
+
+
+1;