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Merged
nakib103 merged 3 commits into from
Aug 3, 2026
+118 −31
Merged

Update to support new DB structure with multiple pockets. #851

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bfad3fa
update to support new db structure with multiple pockets. works on ol…
jamie-m-a Jul 27, 2026
ec4ecf5
fixing some vcf format issues, align with other output
jamie-m-a Aug 3, 2026
2c0d2e2
missed the pipe...
jamie-m-a Aug 3, 2026
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149 changes: 118 additions & 31 deletions ProtVar.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -134,12 +134,42 @@ sub new {

$self->{initial_pid} = $$;

$self->{dbh} = DBI->connect( "dbi:SQLite:dbname=" . $self->{db}, "", "" );
$self->{get_sth} = $self->{dbh}->prepare("SELECT md5, item, matrix FROM consequences WHERE md5 = ?");
$self->prepare_db_statements();

return $self;
}

sub prepare_db_statements {
my ($self) = @_;

$self->{dbh} ||= DBI->connect(
"dbi:SQLite:dbname=" . $self->{db},
"",
"",
{ RaiseError => 1, PrintError => 0, AutoCommit => 1 }
);
$self->{get_sth} = $self->{dbh}->prepare("SELECT md5, item, matrix FROM consequences WHERE md5 = ?");
$self->prepare_pocket_statements() if $self->{pocket};
}

sub prepare_pocket_statements {
my ($self) = @_;

$self->{pocket_attrib_sth} = $self->{dbh}->prepare(
"SELECT score, MpLDDT, energy, burriedness, RoG, residues FROM pocket_attribs WHERE md5 = ? AND pocket_id = ?"
);

my ($has_pocket_residues) = $self->{dbh}->selectrow_array(
"SELECT 1 FROM sqlite_master WHERE type = 'table' AND name = 'pocket_residues'"
);

$self->{pocket_residue_sth} = $has_pocket_residues
? $self->{dbh}->prepare(
"SELECT pocket_id FROM pocket_residues WHERE md5 = ? AND pos = ?"
)
: undef;
}

sub feature_types {
return ['Transcript'];
}
Expand All @@ -154,11 +184,11 @@ sub get_header_info {
}

if ( defined $self->{pocket} ) {
$header{ProtVar_pocket} = "Information about overlapping protein pocket. Output field(s) include: ";
$header{ProtVar_pocket} = "Information about overlapping protein pocket. Output records are separated by '|'; ";
$header{ProtVar_pocket} .=
$self->{config}->{output_format} eq "vcf"
? "(fields are separated by '&') "
: "(fields are separated by ',') ";
? "fields within each record are separated by '&'. Field(s) include: "
: "fields within each record are separated by ','. Field(s) include: ";
$header{ProtVar_pocket} .= "id - Pocket id, ";
$header{ProtVar_pocket} .= "score - Combined score measuring confidence in pocket (score < 800: low confidence; score 800-900: high confidence; score > 900: very high confidence), ";
$header{ProtVar_pocket} .= "MpLDDT - Mean pLDDT score of all the residues from AlphaFold2 model used to form the pocket, ";
Expand Down Expand Up @@ -239,27 +269,69 @@ sub format_output {
my ( $self, $data, $item ) = @_;

my $result = {};
my @records = ref($data) eq 'ARRAY' ? @$data : ($data);

if ( $self->{output_json} ) {
my %hash;
%hash = map { $_ => $data->{$_} } keys %$data;
$result->{$item} = \%hash;
if ( ref($data) eq 'ARRAY' ) {
$result->{$item} = [
map {
my $record = $_;
+{ map { $_ => $record->{$_} } keys %$record };
} @records
];
}
else {
my %hash;
%hash = map { $_ => $data->{$_} } keys %$data;
$result->{$item} = \%hash;
}
}
else {
my $key = "ProtVar_" . $item;
my @formatted_records;
my $field_delimiter = $self->{config}->{output_format} eq "vcf" ? "&" : ",";
my $record_delimiter = "|";

@nakib103 nakib103 Aug 3, 2026

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record delimiter in vcf would not work here as it is already used as separator between CSQ field , e.g. -
G|missense_variant|MODERATE|...

phenotype with similar output format uses + as field delimiter and & as record delimiter. We can re-use same logic?

@jamie-m-a jamie-m-a Aug 3, 2026

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Yep, switched


# replace comma in pocket residue position to avoid delimiter clash
if ($data->{residues}) {
$data->{residues} =~ s/,/p/g;
$data->{residues} = 'p'.$data->{residues};
foreach my $record (@records) {
my %formatted_data = %$record;

# replace comma in pocket residue position to avoid delimiter clash
if ($formatted_data{residues}) {
$formatted_data{residues} =~ s/,/p/g;
$formatted_data{residues} = 'p'.$formatted_data{residues};
}

push @formatted_records, join($field_delimiter, map { $formatted_data{$_} } @{ $field_order->{$item} });
}

$result->{$key} = join(",", map { $data->{$_} } @{ $field_order->{$item} });
$result->{$key} = join($record_delimiter, @formatted_records);
}

return $result;
}

sub get_pocket_ids {
my ( $self, $md5, $pos, $fallback_id ) = @_;

return ($fallback_id) unless $self->{pocket_residue_sth};

# Matrix positions are 0-based; pocket_residues stores UniProt positions.
# Older generated DBs stored pos with SQLite text affinity, so bind as text.
eval {
my $residue_pos = "" . ( $pos + 1 );
$self->{pocket_residue_sth}->execute( $md5, $residue_pos );
};
return ($fallback_id) if $@;

my @ids;
while ( my $arrayref = $self->{pocket_residue_sth}->fetchrow_arrayref ) {
push @ids, $arrayref->[0];
}

@ids = sort { $a <=> $b } @ids;
return @ids ? @ids : ($fallback_id);
}

sub process_from_db {
my ( $self, $tva ) = @_;

Expand All @@ -279,12 +351,18 @@ sub process_from_db {

# forked, reconnect to DB
if ( $$ != $self->{initial_pid} ) {
$self->{dbh} = DBI->connect( "dbi:SQLite:dbname=" . $self->{db}, "", "" );
$self->{get_sth} = $self->{dbh}->prepare("SELECT md5, item, matrix FROM consequences WHERE md5 = ?");
$self->{dbh} = DBI->connect(
"dbi:SQLite:dbname=" . $self->{db},
"",
"",
{ RaiseError => 1, PrintError => 0, AutoCommit => 1 }
);
$self->prepare_db_statements();

# set this so only do once per fork
$self->{initial_pid} = $$;
}
$self->prepare_db_statements() unless $self->{get_sth};
$self->{get_sth}->execute($md5);

my $result_from_db = {};
Expand Down Expand Up @@ -350,21 +428,30 @@ sub process_from_db {

# format the output
if ($id) {
my $sth2 = $self->{dbh}->prepare( "SELECT score, MpLDDT, energy, burriedness, RoG, residues FROM pocket_attribs WHERE md5 = ? AND pocket_id = ?" );
$sth2->execute($md5, $id);
my ( $score, $MpLDDT, $energy, $burriedness, $RoG, $residues ) = @{ $sth2->fetchrow_arrayref };

my $data = {
id => 'P' . $id,
score => $score,
MpLDDT => $MpLDDT,
energy => $energy,
burriedness => $burriedness,
RoG => $RoG,
residues => $residues
};

my $formatted_output = $self->format_output( $data, $item );
my @pocket_data;
$self->prepare_pocket_statements() unless $self->{pocket_attrib_sth};

foreach my $pocket_id ( $self->get_pocket_ids( $md5, $pos, $id ) ) {
$self->{pocket_attrib_sth}->execute($md5, $pocket_id);
my $attribs = $self->{pocket_attrib_sth}->fetchrow_arrayref;
next unless $attribs;

my ( $score, $MpLDDT, $energy, $burriedness, $RoG, $residues ) = @$attribs;

push @pocket_data, {
id => 'P' . $pocket_id,
score => $score,
MpLDDT => $MpLDDT,
energy => $energy,
burriedness => $burriedness,
RoG => $RoG,
residues => $residues
};
}

next unless @pocket_data;

my $formatted_output = $self->format_output( @pocket_data > 1 ? \@pocket_data : $pocket_data[0], $item );
@$result_from_db{ keys %$formatted_output } = values %$formatted_output;
}
}
Expand Down Expand Up @@ -411,4 +498,4 @@ sub run {
return $self->{output_json} ? { "ProtVar" => $result } : $result;
}

1;
1;