Commit bb3a9456 authored by Steve Trevanion's avatar Steve Trevanion
Browse files

fixes when identifying other stops - 1) ribosomal frameshift ignored, 2) stop...

fixes when identifying other stops -  1) ribosomal frameshift ignored, 2) stop codon being automatically annotated as a seleno and 3) non numerical values in comments
parent 9c7ae961
......@@ -245,6 +245,15 @@ sub check_for_stops {
next TRANS;
}
}
# go no further if there is a ribosomal framshift attribute
foreach my $attrib (@{$trans->get_all_Attributes('_rib_frameshift')}) {
if ($attrib->value) {
$log_object->_save_log('log', '', $gsi, '', $tsi, '', "Skipping $tsi ($tname) since it has a ribosomal frameshift attribute");
next TRANS;
}
}
#$support->log_verbose("Studying transcript $tsi ($tname, $tID)\n",1);
$log_object->_save_log('log_verbose', '', $gsi, '', $tsi, '', "Studying transcript $tsi ($tname, $tID)");
my $peptide;
......@@ -336,8 +345,11 @@ sub check_for_stops {
if ($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
if (
elsif (
defined($found_stops[$i]) && defined($found_stops[$i]->[1]) && ($found_stops[$i]->[1] == $offset)) {
push @annotated_stops, $offset;
}
......@@ -350,9 +362,14 @@ 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) && ($offset=~/^\d+$/)){
$log_object->_save_log('log_warning', '', $gene->stable_id, 'TRANSCRIPT', $tsi, 'VQCT_wrong_selC_coord', "Annotated stop for transcript $tsi ($tname) does not match a TGA codon) [$mod_date]");
if ($offset == length($pseq)) {
$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 {
$log_object->_save_log('log_warning', '', $gene->stable_id, 'TRANSCRIPT', $tsi, 'VQCT_wrong_selC_coord', "Annotated stop for transcript $tsi ($tname) \"$offset\" does not match a TGA codon) [$mod_date]");
push @annotated_stops, $offset;
}
}
$i++;
}
}
......
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