Commit 2b31bf77 authored by Dan Sheppard's avatar Dan Sheppard
Browse files

Fix erroneous warning of unmarked selenoprotein when marked selenoprotein also

has unrelated remark beginning with string "selenocysteine ". Found to be the
case in OTTDART00000030742 for Dec 19th 2011 Havana data-freeze of Zebra fish.
parent b2afd180
......@@ -339,7 +339,13 @@ sub check_for_stops {
$annot_stops=$1;
}
elsif ($text =~ /^$alabel2(.*)/) {
$annot_stops=$1;
my $maybe = $1;
if($maybe =~ /^\s*\d+(\s+\d+)*\s*$/) {
$annot_stops=$maybe;
} else {
$log_object->_save_log('log', '', $gene->stable_id, '', $tsi, '', "Maybe annotated stop in incorrect format, maybe just a remark that happens to begin '$alabel2'".
" -- might need to investigate: '$alabel2$maybe' [$mod_date]");
}
}
}
}
......@@ -349,11 +355,8 @@ sub check_for_stops {
if ($annot_stops){
my $i = 0;
foreach my $offset (split(/\s+/, $annot_stops)) {
if ($offset !~ /^\d+$/) {
$log_object->_save_log('log', '', $gene->stable_id, '', $tsi, '', "Annotated stop for transcript tsi ($tname) is not an integer \"$offset\" - might need to investigate [$mod_date]");
}
#OK if it matches a known stop
elsif (
if (
defined($found_stops[$i]) && defined($found_stops[$i]->[1]) && ($found_stops[$i]->[1] == $offset)) {
push @annotated_stops, $offset;
}
......
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