my ($old, $new) = @_;
my (@old_contents) = @{$old}[1..4];
my ($old_id, $old_length) = ($old->[-1], $old->[-2]);
my (@new_contents) = @{$new}[1..4];
my ($new_id, $new_length) = ($new->[-1], $new->[-2]);
my $old_key = join(q{'=!='}, @old_contents) if defined($old_contents[0]);
my $new_key = join(q{'=!='}, @new_contents);
my $reason_key;
my $possible_reason;
if($old_key && $old_key eq $new_key) {
if($new_length > $old_length) {
$reason_key = 'transcript_length';
}
elsif($new_length < $old_length) {
$reason_key = 'other';
$possible_reason = 'the old transcript length was longer than the new transcript';
}
else {
if( ($new_id cmp $old_id) > 0 ) {
$reason_key = 'other';
$possible_reason = 'the old ID was lexographically lower than the new ID';
}
else {
$reason_key = 'id_ordering';
}
}
}
else {
#If all other keys are equal then we used translation length
if( defined($old->[1]) && join(q{=!=},@{$old}[1..3]) eq join(q{=!=},@{$new}[1..3]) ) {
$reason_key = 'translation_length';
}
#If we have translatable genes and we prefered Havana merged NMD over E/H PC
elsif(
$old->[1] && $new->[1] && #We had translatable genes
$old->[2] == 3 && #Old was an Ensembl/Havana
transcript $new->[2] == 2 && #New was E! Havana merged
$old->[3] == 1 && #Old was a Protein Coding
$new->[3] == 2 && #New was a "NMD"
$blurt !~ /nmd/i #User suppressing this test
) {
$reason_key = 'havana_merge_nmd_over_e_coding';
} elsif (! $old->[1] ) {
# The old canonical transcript was not found.
$reason_key = 'new';
} else {
$reason_key = 'other';
}
}
if($reason_key eq 'other') {
if($possible_reason) {
printf("ERROR: %s -> %s change was wrong because %s. Please investigate\n", $old_id, $new_id, $possible_reason);
}
else {
printf("ERROR: %s -> %s change not due to a known reason. Please investigate\n", $old_id, $new_id);
}
printf("\tURL: www.ensemblgenomes.org/id/%s\n", $old_id);
printf("\tURL: www.ensemblgenomes.org/id/%s\n", $new_id);
printf("\tENC: %s\n", encode_json($old));
printf("\tENC: %s\n", encode_json($new));
print("\tSee Bio::EnsEMBL::Utils::TranscriptSelector::sort_into_canonical_order() POD to decode\n");
}
$reason_count{$reason_key}++;
return;
}
Code:
