Commit 91ae3c0c authored by Dan Sheppard's avatar Dan Sheppard
Browse files

Added option to support genuinely Sec-terminating selenoprotiens in add_selcys checking.

parent 1deb5dbd
......@@ -369,8 +369,10 @@ sub check_for_stops {
if ($offset == length($orig_seq)+1) {
if($seen_transcripts->{$tsi} && $seen_transcripts->{$tsi}->[1] eq 'known-tga-stop') {
$log_object->_save_log('log', '', $gene->stable_id, 'TRANSCRIPT', $tsi, '', "Annotated stop for transcript $tsi ($tname) known to be a stop codon. Ok. [$mod_date]");
} elsif($seen_transcripts->{$tsi} && $seen_transcripts->{$tsi}->[1] eq 'known-terminal-sec') {
$log_object->_save_log('log', '', $gene->stable_id, 'TRANSCRIPT', $tsi, '', "Annotated stop for transcript $tsi ($tname) known to be a terminal Sec. Ok. [$mod_date]");
} else {
$log_object->_save_log('log_warning', '', $gene->stable_id, 'TRANSCRIPT', $tsi, '', "Annotated stop for transcript $tsi ($tname) \"$offset\" matches actual stop codon yet has no entry in script config to disambiguate it. Please investigate and add appropriate entry. [$mod_date]");
$log_object->_save_log('log_warning', '', $gene->stable_id, 'TRANSCRIPT', $tsi, '', "Annotated stop for transcript $tsi ($tname) \"$offset\" matches actual stop codon yet has no entry in script config to disambiguate it. Please investigate and add appropriate entry to config arrays in add_selcys.pl. [$mod_date]");
}
}
else {
......
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