From 0f7f8ef7ac178cd58bf72bf230a2f64b3696a0b5 Mon Sep 17 00:00:00 2001
From: Nathan Johnson <njohnson@ebi.ac.uk>
Date: Thu, 24 Jul 2008 13:31:58 +0000
Subject: [PATCH] added some comments
---
.../probe_mapping/probe2transcript.pl | 27 ++++++++++++++++++-
1 file changed, 26 insertions(+), 1 deletion(-)
diff --git a/misc-scripts/probe_mapping/probe2transcript.pl b/misc-scripts/probe_mapping/probe2transcript.pl
index 75b6e21274..d0972a7731 100644
--- a/misc-scripts/probe_mapping/probe2transcript.pl
+++ b/misc-scripts/probe_mapping/probe2transcript.pl
@@ -16,6 +16,7 @@
#To do
#Remove median & get_date and implement EFGUtils when migrating to eFG
#Add unannotated UTR clipping dependant on nearest neighbour
+#Extend UTRs to default length is they are less than defaults, so long as they don't overlap neighbour, then use annotated if present or clip to neighbour start/end if not, also accounting for default UTRs in the neighbour.
use strict;
@@ -55,6 +56,7 @@ my $max_mismatches = 1;
#What we want is to use annotated else use calc or preset default
#so calc and preset default are mutually exclusive
#but annotated can be used with both
+#shouldn't median be mode?
my $annotated_utrs;
@@ -258,6 +260,21 @@ if($calc_utrs){
$three_utr = $transcript->five_prime_utr;
$five_utr = $transcript->three_prime_utr;
+ #We actually want to extend the potentially conservative ensembl UTRs
+ #to the calculated default if they are shorter, but only if this does
+ #not cause overlap with a neighbouring gene.
+ #Do not implement UTR extension until clipping is in place
+ #This will require knowledge of genomic context
+ #What is fastest solution here?
+ #1. Run in a slice context to fetch all genes, then we know the previous transcript
+ #and can easily access the next transcript
+ #2. Simply generate an extended slice from the transcript and pull back genes
+ #We would have to either do this for every trans or just for the longest
+ #
+ #1 is probably most efficient altho' and will actually reduce the memory usage by
+ #chunking by chromosome
+
+
if(defined $five_utr){
$five_cnt++;
push @five_lengths, $five_utr->length;
@@ -337,6 +354,8 @@ foreach my $transcript (@transcripts) {
#we want to be able to test calc and annotated separatly
my %utr_lengths = %utr_defaults;
+ #Need to rework the logic slightly considering UTRs are included in the transcript start/end if they are annotated.
+
if($annotated_utrs){
my ($method, $utr);
@@ -345,7 +364,10 @@ foreach my $transcript (@transcripts) {
$utr = $transcript->$method;
if(defined $utr){# && $utr->length != 0){
- $utr_lengths{$flank} = $utr->length;
+ #$utr_lengths{$flank} = $utr->length;
+ #Set extend to 0 if there are already included in the transcript
+ #need to rename this hash
+ $utr_lengths{$flank} = 0;
}
else{
$unannotated_utrs{$flank}++;
@@ -355,6 +377,9 @@ foreach my $transcript (@transcripts) {
my $slice = $transcript->feature_Slice();
#my $extended_slice = $slice->expand(0, $utr_length); # this takes account of strand
+
+ #The UTRs are already included in the transcript!!
+ #We only need to extend if we have no annotated UTR.
my $extended_slice = $slice->expand($utr_lengths{'five'}, $utr_lengths{'three'}); # this takes account of strand
--
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