From f0cdbdeace5a284a03f07894d312a6d32dc7e12e Mon Sep 17 00:00:00 2001
From: Kieron Taylor <ktaylor@ebi.ac.uk>
Date: Mon, 24 Sep 2012 10:34:51 +0000
Subject: [PATCH] Added a 'flag' at Genebuilder request to allow them to switch
off collection of NMD choices. They want to investigate these cases. Hacky
job for a hacky script.
---
misc-scripts/canonical_transcripts/reason_changes.pl | 9 ++++++++-
1 file changed, 8 insertions(+), 1 deletion(-)
diff --git a/misc-scripts/canonical_transcripts/reason_changes.pl b/misc-scripts/canonical_transcripts/reason_changes.pl
index f26ae38b99..3bd96cf5b7 100755
--- a/misc-scripts/canonical_transcripts/reason_changes.pl
+++ b/misc-scripts/canonical_transcripts/reason_changes.pl
@@ -9,6 +9,11 @@
# - Transcript length (longest)
# - Translation length (longest)
#
+# A not so normal scenario is the choice of an NMD over an Ensembl protein
+# coder. To emit these in all their glory, add NMD to the command line. e.g.
+#
+# perl reason_changes.pl logfile NMD
+#
# If it was not one of these we will complain bitterly and you should
# investigate. If it is a known reason after investigation, that is an
# allowed scenario, then code it into this script.
@@ -20,6 +25,7 @@ use warnings;
use JSON;
my $file = $ARGV[0];
+my $blurt = $ARGV[1] ;
if(! $file) {
die "Was not given a file. Command is $0 PATH_TO_FILE";
@@ -77,7 +83,8 @@ sub compare {
$old->[2] == 3 && #Old was an Ensembl/Havana transcript
$new->[2] == 2 && #New was E! Havana merged
$old->[3] == 1 && #Old was a Protein Coding
- $new->[3] == 2 #New was a "NMD"
+ $new->[3] == 2 && #New was a "NMD"
+ $blurt !~ /nmd/i #User suppressing this test
) {
$reason_key = 'havana_merge_nmd_over_e_coding';
}
--
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