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Commit e61c7632 authored by Andreas Kusalananda Kähäri's avatar Andreas Kusalananda Kähäri
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Re-write of get_species_and_object_type() with input from Eugene K.

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modules/Bio/EnsEMBL/Registry.pm
+ 67
− 210
View file @ e61c7632
......@@ -2422,232 +2422,89 @@ sub version_check {
=cut
my %stable_id_prefix;
my @nonstandard_prefix_species;
my %prefix_patterns = (
'core' => {
'^%sG\d' => 'Gene', # '%s' will be replaced by the stable ID
'^%sT\d' => 'Transcript', # prefix from the meta table.
'^%sP\d' => 'Translation',
'^%sE\d' => 'Exon', },
'compara' => { '^ENSGT\d' => 'Proteintree', # "gene-tree"
'^ENSFM\d' => 'Family',
'^ENSRT\d' => 'NCTree', # "ncRNA-tree"
},
'variation' => { '^ENSSNP\d' => 'SNP',
'^rs\d' => 'SNP', },
'funcgen' => { '^%sR\d' => 'RegulatoryFeature', }, );
our @allowed_prefixes = (
'ENS', # Standard Ensembl prefix.
# The rest are Ensembl Genomes prefixes.
'EB',
'EPr',
'EF',
'EPl',
'EM', );
my %stable_id_stmts = (
'gene' => "SELECT meta.meta_value "
. "FROM gene_stable_id si "
. "JOIN gene USING (gene_id) "
. "JOIN seq_region USING (seq_region_id) "
. "JOIN coord_system USING (coord_system_id) "
. "JOIN meta USING (species_id) "
. "WHERE si.stable_id = ? "
. "AND meta.meta_key = 'species.production_name'",
'transcript' => "SELECT meta.meta_value "
. "FROM transcript_stable_id si "
. "JOIN transcript USING (transcript_id) "
. "JOIN seq_region USING (seq_region_id) "
. "JOIN coord_system USING (coord_system_id) "
. "JOIN meta USING (species_id) "
. "WHERE si.stable_id = ? "
. "AND meta.meta_key = 'species.production_name'",
'exon' => "SELECT meta.meta_value "
. "FROM exon_stable_id si "
. "JOIN exon USING (exon_id) "
. "JOIN seq_region USING (seq_region_id) "
. "JOIN coord_system USING (coord_system_id) "
. "JOIN meta USING (species_id) "
. "WHERE si.stable_id = ? "
. "AND meta.meta_key = 'species.production_name'",
'translation' => "SELECT meta.meta_value "
. "FROM translation_stable_id si "
. "JOIN translation USING (translation_id) "
. "JOIN transcript USING (transcript_id) "
. "JOIN seq_region USING (seq_region_id) "
. "JOIN coord_system USING (coord_system_id) "
. "JOIN meta USING (species_id) "
. "WHERE si.stable_id = ? "
. "AND meta.meta_key = 'species.production_name'",
);
sub get_species_and_object_type {
my ( $self, $stable_id, $known_type ) = @_;
if ( !%stable_id_prefix ) {
# Fetch stable ID prefixes from all connected databases.
my $dbc;
foreach
my $dba ( @{ $self->get_all_DBAdaptors( '-group' => 'core' ) } )
{
my $species = $dba->species();
if ( lc($species) eq 'multi' ) { next }
if ( !defined($dbc)
|| $dbc->host() ne $dba->dbc()->host()
|| $dbc->dbname() ne $dba->dbc()->dbname() )
{
$dbc = $dba->dbc();
}
my $dbh = $dbc->db_handle();
my $dbname = $dbc->dbname();
my $statement = sprintf(
"SELECT meta_value "
. "FROM %s "
. "WHERE meta_key = 'species.stable_id_prefix' "
. "AND species_id = ?",
$dbh->quote_identifier( undef, $dbname, 'meta' )
);
my $sth = $dbh->prepare($statement);
$sth->{'PrintError'} = 0;
$sth->{'RaiseError'} = 0;
if ( !$sth->execute( $dba->species_id() ) ) { next }
$sth->{'PrintError'} = $dbh->{'PrintError'};
$sth->{'RaiseError'} = $dbh->{'RaiseError'};
my $prefix;
$sth->bind_columns( \($prefix) );
my $fetched_something = 0;
my ( $self, $stable_id, $known_type );
while ( $sth->fetch() ) {
$fetched_something = 1;
my $standard_prefix = 0;
foreach my $allowed_prefix (@allowed_prefixes) {
if ( substr( $prefix, 0, length($allowed_prefix) ) eq
$allowed_prefix )
{
$standard_prefix = 1;
last;
}
}
if ( !$standard_prefix ) {
# These will be further queried if we find no match.
push( @nonstandard_prefix_species, $species );
} else {
if ( !exists( $stable_id_prefix{$prefix} ) ) {
$stable_id_prefix{$prefix} = [$species];
} else {
push( @{ $stable_id_prefix{$prefix} }, $species );
}
}
} ## end while ( $sth->fetch() )
if ( !$fetched_something ) {
# This database didn't have a matching
# 'species.stable_id_prefix' key in its meta table.
push( @nonstandard_prefix_species, $species );
}
if ( defined($known_type)
&& !exists( $stable_id_stmts{ lc($known_type) } ) )
{
throw( sprintf( "Got invalid known_type '%s'", $known_type ) );
}
} ## end foreach my $dba ( @{ $self->get_all_DBAdaptors...})
} ## end if ( !%stable_id_prefix)
my @types = ( defined($known_type)
? ($known_type)
: ( 'Gene', 'Transcript', 'Translation', 'Exon' ) );
my @match;
FIRSTLOOP:
foreach my $group ( keys(%prefix_patterns) ) {
foreach my $prefix_pattern ( keys( %{ $prefix_patterns{$group} } ) )
{
my $type = $prefix_patterns{$group}{$prefix_pattern};
if ( index( $prefix_pattern, '%s' ) == -1 ) {
# The prefix pattern does not contain '%s', so we need not
# insert the stable ID prefixes read from the meta tables.
my $dbc;
my $complete_pattern = $prefix_pattern;
if ( $stable_id =~ /$complete_pattern/ ) {
@match = ( 'multi', $type, $group );
last FIRSTLOOP;
}
} else {
# The prefix pattern contain '%s' which needs to be replaced
# with the stable ID prefix read from the meta table of each
# core database.
foreach my $prefix ( keys %stable_id_prefix ) {
my $species_array = $stable_id_prefix{$prefix};
my $complete_pattern = sprintf( $prefix_pattern, $prefix );
if ( $stable_id =~ /$complete_pattern/ ) {
if ( scalar( @{$species_array} ) == 1 ) {
# Only one species possible for this prefix pattern.
@match = ( $species_array->[0], $type, $group );
last FIRSTLOOP;
} else {
# More than one possible species for this prefix pattern.
foreach my $species ( @{$species_array} ) {
my $adaptor =
$self->get_adaptor( $species, $group, $type );
my $object = $adaptor->fetch_by_stable_id($stable_id);
if ( defined($object) ) {
@match = ( $species, $type, $group );
last FIRSTLOOP;
}
}
}
}
} ## end foreach my $prefix ( keys %stable_id_prefix)
} ## end else [ if ( index( $prefix_pattern...))]
OUTER:
foreach
my $dba ( @{ $self->get_all_DBAdaptors( '-group' => 'Core' ) } )
{
if ( !defined($dbc)
|| !( $dbc->host() eq $dba->dbc()->host()
&& $dbc->dbname() eq $dba->dbc()->dbname() ) )
{
$dbc = $dba->dbc();
}
} ## end foreach my $prefix_pattern ...
} ## end foreach my $group ( keys(%prefix_patterns...))
my $dbh = $dbc->db_handle();
if (@match) { return @match }
foreach my $type (@types) {
my $sth = $dbh->prepare( $stable_id_stmts{ lc($type) } );
# Go through the species in @nonstandard_prefix_species and query them
# for genes, transcripts, etc. (only core objects) until we have found
# a match for our stable ID or until we have exhausted the list.
$sth->bind_param( 1, $stable_id, SQL_VARCHAR );
$sth->execute();
SECONDLOOP:
foreach my $species (@nonstandard_prefix_species) {
my $species = $sth->fetchall_arrayref()->[0][0];
my $dbc;
$sth->finish();
foreach my $dba ( @{$self->get_all_DBAdaptors('-group' => 'core',
'-species' => $species
) } )
{
if ( !defined($dbc)
|| $dbc->host() ne $dba->dbc()->host()
|| $dbc->dbname() ne $dba->dbc()->dbname() )
{
$dbc = $dba->dbc();
if ( defined($species) ) {
@match = ( $species, $type, 'Core' );
last OUTER;
}
}
my $dbh = $dbc->db_handle();
my $dbname = $dbc->dbname();
foreach my $type ( defined($known_type) ? $known_type : 'Gene',
'Transcript', 'Translation', 'Exon' )
{
my $type_lc = lc($type);
my $statement =
sprintf( "SELECT COUNT(1) "
. "FROM %s si "
. "JOIN %s USING (%s) "
. "JOIN seq_region USING (seq_region_id) "
. "JOIN coord_system cs USING (coord_system_id) "
. "WHERE si.stable_id = ? "
. "AND cs.species_id = ?",
$dbh->quote_identifier(
undef, $dbname,
sprintf( "%s_stable_id", $type_lc ) ),
$dbh->quote_identifier( undef, $dbname, $type_lc ),
$dbh->quote_identifier(
undef, $dbname, sprintf( "%s_id", $type_lc )
) );
my $sth = $dbh->prepare($statement);
$sth->bind_param( 1, $stable_id, SQL_VARCHAR );
$sth->bind_param( 1, $dba->species_id(), SQL_INTEGER );
$sth->execute();
my $count = $sth->fetchall_arrayref()->[0][0];
$sth->finish();
if ( defined($count) && $count > 0 ) {
@match = ( $species, $type, 'Core' );
last SECONDLOOP;
}
} ## end foreach my $type ( defined(...))
} ## end foreach my $dba ( @{ $self->get_all_DBAdaptors...})
} ## end foreach my $species (@nonstandard_prefix_species)
} ## end foreach my $dba ( @{ $self->get_all_DBAdaptors...})
return @match;
} ## end sub get_species_and_object_type
......
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