From 441627a16cd5c50e9f346343b58509010689f2de Mon Sep 17 00:00:00 2001
From: Steve Trevanion <st3@sanger.ac.uk>
Date: Fri, 6 Mar 2009 18:09:21 +0000
Subject: [PATCH] added gene name to stop codon report
---
modules/Bio/EnsEMBL/Utils/VegaCuration/Translation.pm | 7 ++++---
1 file changed, 4 insertions(+), 3 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Utils/VegaCuration/Translation.pm b/modules/Bio/EnsEMBL/Utils/VegaCuration/Translation.pm
index b9b196dba7..79f3dd9ad9 100644
--- a/modules/Bio/EnsEMBL/Utils/VegaCuration/Translation.pm
+++ b/modules/Bio/EnsEMBL/Utils/VegaCuration/Translation.pm
@@ -188,6 +188,7 @@ sub get_havana_seleno_comments {
sub check_for_stops {
my $support = shift;
my ($gene,$seen_transcripts) = @_;
+ my $gname = $gene->get_all_Attributes('name')->[0]->value;
my $scodon = 'TGA';
my $mod_date = $support->date_format( $gene->modified_date,'%d/%m/%y' );
@@ -242,10 +243,10 @@ sub check_for_stops {
#...no - an internal stop codon error in the database...
if ($num_tga < $num_stops) {
if ($source eq 'havana') {
- $support->log_warning("INTERNAL STOPS HAVANA: Transcript $tsi ($tname) has non \'$scodon\' stop codons [$mod_date]:\nSequence = $orig_seq\nStops at $positions)\n\n");
+ $support->log_warning("INTERNAL STOPS HAVANA: Transcript $tsi ($tname) from gene $gname has non \'$scodon\' stop codons [$mod_date]:\nSequence = $orig_seq\nStops at $positions)\n\n");
}
else {
- $support->log_warning("INTERNAL STOPS EXTERNAL: Transcript $tsi ($tname) has non \'$scodon\' stop codons[$mod_date]:\nSequence = $orig_seq\nStops at $positions)\n\n");
+ $support->log_warning("INTERNAL STOPS EXTERNAL: Transcript $tsi ($tname) from gene $gname has non \'$scodon\' stop codons[$mod_date]:\nSequence = $orig_seq\nStops at $positions)\n\n");
}
}
@@ -315,7 +316,7 @@ sub check_for_stops {
$support->log_verbose("Transcript $tsi ($tname) has potential selenocysteines but has been discounted by annotators:\n\t".$seen_transcripts->{$tsi}.") [$mod_date]\n");
}
else {
- $support->log("POTENTIAL SELENO ($seq) in $tsi ($tname) found at $pos) [$mod_date]\n");
+ $support->log("POTENTIAL SELENO ($seq) in $tsi ($tname, gene $gname) found at $pos [$mod_date]\n");
}
}
}
--
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