Skip to content

Add prefix consistency check #646

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
Parent: fixing StrainType check to allow for "isolate"
wants to merge 2 commits into
base: release/mvp
Choose a base branch
from
Open

Add prefix consistency check #646

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
5316a4d
updated Stable ID check to check that all prefixes per features are c…
leannehaggerty Aug 13, 2025
d7b9e92
add license back
leannehaggerty Aug 13, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
159 changes: 126 additions & 33 deletions lib/Bio/EnsEMBL/DataCheck/Checks/GeneStableID.pm
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -28,72 +28,74 @@ use Bio::EnsEMBL::DataCheck::Test::DataCheck;
extends 'Bio::EnsEMBL::DataCheck::DbCheck';

use constant {
NAME => 'GeneStableID',
DESCRIPTION => 'Genes, transcripts, exons and translations have non-NULL, unique stable IDs',
GROUPS => ['core', 'brc4_core', 'geneset'],
DB_TYPES => ['core'],
TABLES => ['coord_system', 'exon', 'gene', 'seq_region', 'transcript', 'translation']
NAME => 'GeneStableID',
DESCRIPTION => 'Genes, transcripts, exons and translations have non-NULL, unique stable IDs and consistent ID base prefixes',
GROUPS => ['core', 'brc4_core', 'geneset'],
DB_TYPES => ['core'],
TABLES => ['coord_system', 'exon', 'gene', 'seq_region', 'transcript', 'translation']
};

sub tests {
my ($self) = @_;
my $species_id = $self->dba->species_id;
my ($self) = @_;
my $species_id = $self->dba->species_id;

$self->stable_id_check('gene', $species_id);
$self->stable_id_check('transcript', $species_id);
$self->stable_id_check('exon', $species_id);
$self->stable_id_check('gene', $species_id);
$self->stable_id_check('transcript', $species_id);
$self->stable_id_check('exon', $species_id);
$self->translation_stable_id_check($species_id);
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Need to check this for metazoa/plants data. Most likely is not true for microbes if translations have the same sequences, as they are using sequence derived hashes as IDs.
Upd. Checked. Seems to be hold.


$self->translation_stable_id_check($species_id);
# NEW: check base prefix consistency across feature types
$self->stable_id_prefix_consistency_check($species_id);
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Could you condition it with a genebuild.method ?
Like we have it here

ensembl-datacheck/lib/Bio/EnsEMBL/DataCheck/Checks/GeneSymbols.pm

Line 39 in 676250c

SKIP: {

}

sub stable_id_check {
my ($self, $table, $species_id) = @_;
my ($self, $table, $species_id) = @_;

my $desc_1 = $table.' table has non-NULL stable IDs';
my $diag_1 = "Null $table.stable_id";
my $sql_1 = qq/
my $desc_1 = $table.' table has non-NULL stable IDs';
my $diag_1 = "Null $table.stable_id";
my $sql_1 = qq/
SELECT $table.stable_id FROM
$table INNER JOIN
seq_region sr USING (seq_region_id) INNER JOIN
coord_system cs USING (coord_system_id)
WHERE cs.species_id = $species_id
AND $table.stable_id IS NULL
/;
is_rows_zero($self->dba, $sql_1, $desc_1, $diag_1);
/;
is_rows_zero($self->dba, $sql_1, $desc_1, $diag_1);

my $desc_2 = $table.' table has unique stable IDs';
my $diag_2 = "Duplicate $table.stable_id";
my $sql_2 = qq/
my $desc_2 = $table.' table has unique stable IDs';
my $diag_2 = "Duplicate $table.stable_id";
my $sql_2 = qq/
SELECT $table.stable_id FROM
$table INNER JOIN
seq_region sr USING (seq_region_id) INNER JOIN
coord_system cs USING (coord_system_id)
WHERE cs.species_id = $species_id
GROUP BY $table.stable_id
HAVING COUNT(*) > 1
/;
is_rows_zero($self->dba, $sql_2, $desc_2, $diag_2);
/;
is_rows_zero($self->dba, $sql_2, $desc_2, $diag_2);
}

sub translation_stable_id_check {
my ($self, $species_id) = @_;
my ($self, $species_id) = @_;

my $desc_1 = 'translation table has non-NULL stable IDs';
my $diag_1 = "Null translation.stable_id";
my $sql_1 = qq/
my $desc_1 = 'translation table has non-NULL stable IDs';
my $diag_1 = "Null translation.stable_id";
my $sql_1 = qq/
SELECT tn.stable_id FROM
translation tn INNER JOIN
transcript tt USING (transcript_id) INNER JOIN
seq_region sr USING (seq_region_id) INNER JOIN
coord_system cs USING (coord_system_id)
WHERE cs.species_id = $species_id
AND tn.stable_id IS NULL
/;
is_rows_zero($self->dba, $sql_1, $desc_1, $diag_1);
/;
is_rows_zero($self->dba, $sql_1, $desc_1, $diag_1);

my $desc_2 = 'translation table has unique stable IDs';
my $diag_2 = "Duplicate translation.stable_id";
my $sql_2 = qq/
my $desc_2 = 'translation table has unique stable IDs';
my $diag_2 = "Duplicate translation.stable_id";
my $sql_2 = qq/
SELECT tn.stable_id FROM
translation tn INNER JOIN
transcript tt USING (transcript_id) INNER JOIN
Expand All @@ -103,8 +105,99 @@ sub translation_stable_id_check {
AND cs.name <> 'lrg'
GROUP BY tn.stable_id
HAVING COUNT(*) > 1
/;
is_rows_zero($self->dba, $sql_2, $desc_2, $diag_2);
/;
is_rows_zero($self->dba, $sql_2, $desc_2, $diag_2);
}

# -------------------------------
# NEW: prefix consistency checker
# -------------------------------
sub stable_id_prefix_consistency_check {
my ($self, $species_id) = @_;

my %tables = (
gene => 'G',
transcript => 'T',
exon => 'E',
translation=> 'P',
);

my %prefixes_by_table;
for my $table (keys %tables) {
$prefixes_by_table{$table} = $self->get_base_prefixes_for_table($table, $species_id, $tables{$table});
}

# Union of all base prefixes observed across all feature types
my %union;
for my $table (keys %prefixes_by_table) {
$union{$_}++ for @{$prefixes_by_table{$table}};
}
my @all_prefixes = sort keys %union;

my $desc = 'Stable ID base prefix is consistent across genes, transcripts, exons and translations';
my $ok = @all_prefixes <= 1;

# If not OK, provide diagnostics by table
unless ($ok) {
my $diag = "Observed base prefixes per table:\n";
for my $table (sort keys %prefixes_by_table) {
my @vals = @{$prefixes_by_table{$table}};
@vals = ('<none>') unless @vals;
$diag .= sprintf(" %-12s : %s\n", $table, join(', ', sort @vals));
}
diag($diag);
}

ok($ok, $desc);
}

# Helper: collect DISTINCT base prefixes for a table.
# Base prefix: (letters/underscore)* BEFORE the feature-type letter (G/T/E/P) that precedes the numeric part.
# We strip any ".version" first (in SQL), then use Perl regex to normalise.
sub get_base_prefixes_for_table {
my ($self, $table, $species_id, $feature_letter) = @_;

my $sql;
if ($table eq 'translation') {
# translation -> transcript -> seq_region -> coord_system
$sql = qq/
SELECT DISTINCT SUBSTRING_INDEX(tn.stable_id, '.', 1) AS sid
FROM translation tn
INNER JOIN transcript tt USING (transcript_id)
INNER JOIN seq_region sr USING (seq_region_id)
INNER JOIN coord_system cs USING (coord_system_id)
WHERE cs.species_id = $species_id
AND tn.stable_id IS NOT NULL
/;
} else {
# gene, transcript, exon all carry seq_region_id
$sql = qq/
SELECT DISTINCT SUBSTRING_INDEX($table.stable_id, '.', 1) AS sid
FROM $table
INNER JOIN seq_region sr USING (seq_region_id)
INNER JOIN coord_system cs USING (coord_system_id)
WHERE cs.species_id = $species_id
AND $table.stable_id IS NOT NULL
/;
}

my $dbh = $self->dba->dbc->db_handle;
my $sth = $dbh->prepare($sql);
$sth->execute();

my %seen;
while (my ($sid) = $sth->fetchrow_array) {
next unless defined $sid && $sid ne '';

# drop trailing digits and optional feature-type letter; ignore version (already stripped in SQL)
$sid =~ s/\d+$//; # ENSG00000123 -> ENSG
$sid =~ s/[GTEP]$//i; # remove trailing feature-type letter (G/T/E/P), if present

$seen{$sid}++ if $sid ne '';
}

return [ sort keys %seen ];
}


1;