Commit 4551e854 authored by Dan Sheppard's avatar Dan Sheppard
Browse files

Selenoprotein QC fixes for vega.

1. Fix check_for_stops to cope with multiple adjacent internal stops without a loss of codon to AA sync.
Found when running add_selcys.pl on zebrafish for Vega 47.

2. Fix to existing conditional in vega Sec QC script which tests for an anacode bug before deciding to complain
about missing Sec markup for selenoproteins that also stop with TGA, so that this conditional actually spots
this case in more proteins and so cries wolf less often.
parent 4038e502
......@@ -272,7 +272,7 @@ sub check_for_stops {
my $mrna = $trans->translateable_seq;
my $offset = 0;
my $tstop;
while ($pseq =~ /([^\*]+)\*(.*)/) {
while ($pseq =~ /^([^\*]*)\*(.*)/) {
my $pseq1_f = $1;
$pseq = $2;
my $seq_flag = 0;
......@@ -362,7 +362,7 @@ sub check_for_stops {
$log_object->_save_log('log_warning', '', $gene->stable_id, 'PEPTIDE', $tsi, 'VQCT_wrong_selC_coord', "PEPTIDE: Annotated stop for transcript $tsi ($tname) is out by one) [$mod_date]");
}
elsif (defined($offset) && ($offset=~/^\d+$/)){
if ($offset == length($pseq)) {
if ($offset == length($orig_seq)+1) {
$log_object->_save_log('log', '', $gene->stable_id, 'TRANSCRIPT', $tsi, '', "Annotated stop for transcript $tsi ($tname) \"$offset\" matches actual stop codon, sounds like an anacode bug to me [$mod_date]");
}
else {
......
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