From 3b9a7d3cb0b635a3f1271dff7e429dd9ca7c4762 Mon Sep 17 00:00:00 2001
From: Kieron Taylor <ktaylor@ebi.ac.uk>
Date: Wed, 7 Nov 2012 15:05:50 +0000
Subject: [PATCH] Added support for situations where original canonical
transcripts have disappeared from the data.
---
misc-scripts/canonical_transcripts/reason_changes.pl | 6 ++++--
.../select_canonical_transcripts.pl | 9 ++++++++-
2 files changed, 12 insertions(+), 3 deletions(-)
diff --git a/misc-scripts/canonical_transcripts/reason_changes.pl b/misc-scripts/canonical_transcripts/reason_changes.pl
index 3bd96cf5b7..764d88da9e 100755
--- a/misc-scripts/canonical_transcripts/reason_changes.pl
+++ b/misc-scripts/canonical_transcripts/reason_changes.pl
@@ -87,8 +87,10 @@ sub compare {
$blurt !~ /nmd/i #User suppressing this test
) {
$reason_key = 'havana_merge_nmd_over_e_coding';
- }
- else {
+ } elsif (! $old->[1] ) {
+ # The old canonical transcript was not found.
+ $reason_key = 'new';
+ } else {
$reason_key = 'other';
}
}
diff --git a/misc-scripts/canonical_transcripts/select_canonical_transcripts.pl b/misc-scripts/canonical_transcripts/select_canonical_transcripts.pl
index 8a7448e278..fe072dc28b 100644
--- a/misc-scripts/canonical_transcripts/select_canonical_transcripts.pl
+++ b/misc-scripts/canonical_transcripts/select_canonical_transcripts.pl
@@ -144,7 +144,13 @@ foreach my $slice (@$slices) {
my $old_canonical = $gene->canonical_transcript;
- if ($new_canonical->dbID != $old_canonical->dbID) {
+ if (! defined($old_canonical)) {
+ # Original canonical transcript is now absent, or never set.
+ if ($log_fh) {
+ print $log_fh "Old=[,,,,,,]\n";
+ printf $log_fh "New=[%s,%s,%s,%s,%s,%s,'%s']\n", @{ $transcript_selector->encode_transcript($new_canonical) };
+ }
+ } elsif ($new_canonical->dbID != $old_canonical->dbID) {
no warnings 'uninitialized';
printf "%s (%s) changed transcript from %s (%s) to %s (%s)\n",
$gene->stable_id,$gene->dbID,$old_canonical->stable_id,$old_canonical->dbID,
@@ -166,6 +172,7 @@ foreach my $slice (@$slices) {
printf $log_fh "New=[%s,%s,%s,%s,%s,%s,'%s']\n", @{ $transcript_selector->encode_transcript($new_canonical) };
}
}
+
}
}
--
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