Raw content of Bio::EnsEMBL::Compara::DBSQL::AnchorAlignAdaptor
<![CDATA[=head1 NAME
Bio::EnsEMBL::Compara::Production::DBSQL::AnchorAlignAdaptor
=head1 SYNOPSIS
=head1 CONTACT
Jessica Severin : jessica@ebi.ac.uk
=head1 APPENDIX
=cut
package Bio::EnsEMBL::Compara::DBSQL::AnchorAlignAdaptor;
use Data::Dumper;
use Bio::EnsEMBL::Compara::Production::EPOanchors::AnchorAlign;
use Bio::EnsEMBL::Hive::DBSQL::AnalysisDataAdaptor;
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
our @ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);
#############################
#
# store methods
#
#############################
=head2 store
Arg[1] : one or many DnaFragChunk objects
Example : $adaptor->store($chunk);
Description: stores DnaFragChunk objects into compara database
Returntype : none
Exceptions : none
Caller : general
=cut
sub store {
my ($self, $anchor_align) = @_;
throw() unless($anchor_align);
throw() unless(UNIVERSAL::isa($anchor_align, 'Bio::EnsEMBL::Compara::Production::AnchorAlign'));
my $query = qq{
INSERT INTO anchor_align
(method_link_species_set_id, anchor_id, dnafrag_id, dnafrag_start,
dnafrag_end, dnafrag_strand, score, num_of_organisms, num_of_sequences)
VALUES (?,?,?,?,?,?,?,?,?)};
my $sth = $self->prepare($query);
my $insertCount =
$sth->execute($anchor_align->method_link_species_set_id,
$anchor_align->anchor_id,
$anchor_align->dnafrag_id,
$anchor_align->dnafrag_start,
$anchor_align->dnafrag_end,
$anchor_align->dnafrag_strand,
$anchor_align->score,
$anchor_align->num_of_organisms,
$anchor_align->num_of_sequences,
);
if($insertCount>0) {
#sucessful insert
$anchor_align->dbID( $sth->{'mysql_insertid'} );
$sth->finish;
}
$anchor_align->adaptor($self);
return $anchor_align;
}
sub store_exonerate_hits {
my $self = shift;
my $batch_records = shift;
throw() unless($batch_records);
my $dcs = $self->dbc->disconnect_when_inactive();
$self->dbc->disconnect_when_inactive(0);
$self->dbc->do("LOCK TABLE anchor_align WRITE");
my $query = qq{
INSERT INTO anchor_align (method_link_species_set_id, anchor_id, dnafrag_id, dnafrag_start,
dnafrag_end, dnafrag_strand, score, num_of_organisms, num_of_sequences)
VALUES (?,?,?,?,?,?,?,?,?)};
my $sth = $self->prepare($query);
foreach my $row(@$batch_records) {
$sth->execute( split(":", $row) );
}
$sth->finish;
$self->dbc->do("UNLOCK TABLES");
$self->dbc->disconnect_when_inactive($dcs);
return 1;
}
=head2 store_new_method_link_species_set_id
Arg[1] :
Example :
Description:
Returntype : none
Exceptions : none
Caller : general
=cut
#sub store_new_method_link_species_set_id {
# my($self) = @_;
# my $insert_sth = "insert into method_link
###############################################################################
#
# fetch methods
#
###############################################################################
=head2 fetch_dnafrag_id
Arg[1] :
Arg[2] :
Example :
Description:
Returntype :
Exceptions : none
Caller : general
=cut
sub fetch_dnafrag_id {
my $self = shift;
my($coord_sys, $dnafrag_name, $target_genome_db_id) = @_;
unless (defined($coord_sys) and defined($dnafrag_name) and defined($target_genome_db_id)) {
throw("fetch_dnafrag_id must have a coord_sys, dnafrag_name and target_genome_db_id");
}
my $query = qq{
SELECT dnafrag_id FROM dnafrag WHERE name = ? AND
coord_system_name = ? AND genome_db_id = ?};
my $sth = $self->prepare($query);
$sth->execute($dnafrag_name, $coord_sys, $target_genome_db_id) or die $self->errstr;
while (my$row = $sth->fetchrow_arrayref) {
return $row->[0];
}
}
##########################
sub get_target_file {
my $self = shift;
my($analysis_data_id, $target_genome_db_id) = @_;
my $query = qq{
SELECT data FROM analysis_data WHERE analysis_data = ?};
my $sth = $self->prepare($query);
$sth->execute($analysis_data_id) or die $self->errstr;
return $sth->fetchrow_arrayref()->[0]->{target_genomes}->{$target_genome_db_id};
}
=head2 fetch_anchors_by_genomedb_id
Arg[1] :
Arg[2] :
Example :
Description:
Returntype :
Exceptions : none
Caller : general
=cut
sub fetch_anchors_by_genomedb_id {
my ($self, $genome_db_id) = @_;
my $return_hashref;
unless (defined $genome_db_id) {
throw("fetch_all_by_anchor_id_and_mlss_id must have an anchor_id and a method_link_species_set_id");
}
my $query = qq{
SELECT aa.dnafrag_id, aa.anchor_align_id, aa.anchor_id,
aa.dnafrag_start, aa.dnafrag_end
FROM anchor_align aa INNER JOIN dnafrag df ON
aa.dnafrag_id = df.dnafrag_id WHERE
df.genome_db_id = ? order by aa.dnafrag_id, aa.dnafrag_start};
my $sth = $self->prepare($query);
$sth->execute($genome_db_id) or die $self->errstr;
while (my$row = $sth->fetchrow_arrayref) {
push(@{$return_hashref->{$row->[0]}}, [ $row->[1], $row->[2], $row->[3], $row->[4] ]);
}
return $return_hashref;
}
=head2 fetch_all_by_anchor_id_and_mlss_id
Arg[1] : anchor_id, string
Arg[2] : method_link_species_set_id, string
Example : my $anchor = $anchor_align_adaptor->fetch_all_by_anchor_id_and_mlss_id($self->input_anchor_id,$self->method_link_species_set_id);
Description: returns hashref of cols. from anchor_align table using anchor_align_id as unique hash key
Returntype : hashref
Exceptions : none
Caller : general
=cut
sub fetch_all_by_anchor_id_and_mlss_id {
my ($self, $anchor_id, $method_link_species_set_id) = @_;
unless (defined $anchor_id && defined $method_link_species_set_id) {
throw("fetch_all_by_anchor_id_and_mlss_id must have an anchor_id and a method_link_species_set_id");
}
my $query = qq{
SELECT anchor_align_id, method_link_species_set_id, anchor_id,
dnafrag_id, dnafrag_start, dnafrag_end, dnafrag_strand, score,
num_of_organisms, num_of_sequences FROM anchor_align WHERE
anchor_id = ? AND method_link_species_set_id = ?};
my $sth = $self->prepare($query);
$sth->execute($anchor_id, $method_link_species_set_id) or die $self->errstr;
return $sth->fetchall_hashref("anchor_align_id");
}
=head2 fetch_dnafrag_and_genome_db_ids_by_test_mlssid
Arg[1] : method_link_species_set_id, string
Arg[2] : genome_db_ids, arrray_ref
Example : my $anchor = $anchor_align_adaptor->fetch_all_by_anchor_id_and_mlss_id($self->input_anchor_id,$self->method_link_species_set_id);
Description: returns hashref of cols. from anchor_align table using anchor_align_id as unique hash key
Returntype : hashref
Exceptions : none
Caller : general
=cut
sub fetch_dnafrag_and_genome_db_ids_by_test_mlssid {
my ($self, $test_method_link_species_set_id, $anchor_id) = @_;
unless (defined $test_method_link_species_set_id && defined $anchor_id) {
throw("fetch_dnafrag_and_genome_db_ids_by_test_mlssid
must have a method_link_species_set_id and an anchor_id");
}
# my $question_marks = join(",", split("","?" x scalar(@$genome_db_ids)));
my $query = qq{
SELECT aa.dnafrag_id, df.genome_db_id
FROM anchor_align aa INNER JOIN dnafrag df on aa.dnafrag_id = df.dnafrag_id
WHERE aa.anchor_id = ? and aa.method_link_species_set_id = ? AND aa.anchor_status IS NULL};
# df.genome_db_id IN ($question_marks) AND aa.anchor_status IS NULL};
my $sth = $self->prepare($query);
my $genome_dbs = join(",", @$genome_db_ids);
$sth->execute($anchor_id, $test_method_link_species_set_id, @$genome_db_ids) or die;
return $sth->fetchall_arrayref;
}
=head2 fetch_all_anchor_ids_by_test_mlssid_and_genome_db_ids
Arg[1] : method_link_species_set_id, string
Arg[2] : genome_db_ids, arrray_ref
Arg[3] : anchor_id, string
Example : my $anchor = $anchor_align_adaptor->fetch_all_by_anchor_id_and_mlss_id($self->input_anchor_id,$self->method_link_species_set_id);
Description: returns hashref of cols. from anchor_align table using anchor_align_id as unique hash key
Returntype : hashref
Exceptions : none
Caller : general
=cut
sub fetch_all_anchor_ids_by_test_mlssid_and_genome_db_ids {
my ($self, $test_method_link_species_set_id) = @_;
unless (defined $test_method_link_species_set_id) {
throw("fetch_all_anchor_ids_by_test_mlssid_and_genome_db_ids
must have a method_link_species_set_id");
}
# my $question_marks = join(",", split("","?" x scalar(@$genome_db_ids)));
my $query = qq{
SELECT distinct(aa.anchor_id)
FROM anchor_align aa INNER JOIN dnafrag df on aa.dnafrag_id = df.dnafrag_id
WHERE aa.method_link_species_set_id = ?};
# df.genome_db_id IN ($question_marks) AND aa.anchor_status IS NULL};
my $sth = $self->prepare($query);
my $genome_dbs = join(",", @$genome_db_ids);
$sth->execute($test_method_link_species_set_id) or die $self->errstr;
return $sth->fetchall_arrayref;
}
=head2 fetch_all_anchors_with_zero_strand
Arg[1] : genome_db_ids, array_reff
Arg[2] : method_link_species_set_id, string
Example : my $anchor = $anchor_align_adaptor->fetch_all_anchors_with_zero_strand($self->genome_db_ids, $self->test_method_link_species_set_id);
Description: returns arrayref of anchor_id's. from anchor_align table
Returntype : hashref
Exceptions : none
Caller : general
=cut
sub fetch_all_anchors_with_zero_strand {
my ($self, $method_link_species_set_id) = @_;
unless (defined $method_link_species_set_id) {
throw("fetch_all_anchors_with_zero_strand must have a method_link_species_set_id");
}
# my $question_marks = join(",", split("","?" x scalar(@$genome_db_ids)));
my $query = qq{
SELECT distinct(aa.anchor_id) from anchor_align aa INNER JOIN dnafrag df
ON aa.dnafrag_id = df.dnafrag_id WHERE aa.dnafrag_strand = 0 AND
aa.method_link_species_set_id = ? AND aa.anchor_status IS NULL};
my $sth = $self->prepare($query);
my $genome_dbs = join(",", @$genome_db_ids);
$sth->execute($method_link_species_set_id, @$genome_db_ids) or die $self->errstr;
return $sth->fetchall_arrayref;
}
=head2 update_zero_strand_anchors
Arg[1] : anchor_ids, arrayref
Arg[2] : analysis_id, string
Arg[3] : method_link_species_set_id, string
Example :
Description:
Returntype :
Exceptions : none
Caller : general
=cut
sub update_zero_strand_anchors {
my ($self, $anchor_ids, $analysis_id, $method_link_species_set_id) = @_;
unless (defined $anchor_ids && defined $analysis_id && defined $method_link_species_set_id) {
throw("update_anchors_with_zero_strand must have a list of anchor_ids, an analysis_id and a method_link_species_set_id");
}
my $query = qq{update anchor_align set anchor_status = ? where method_link_species_set_id = ? and anchor_id = ?};
my $sth = $self->prepare($query);
foreach my$anchor_id(@{$anchor_ids}) {
$sth->execute($analysis_id, $method_link_species_set_id, $anchor_id->[0]) or die $self->errstr;
}
}
=head2 update_failed_anchor
Arg[1] : anchor_id, hashref
Arg[2] : current analysis_id, string
Example : $anchor_align_adaptor->update_failed_anchor($self->input_anchor_id, $self->input_analysis_id);
Description: updates anchor_status field, setting it to the current analysis_id, if the anchor fails the filters associated with the analysis_id
Returntype : none
Exceptions : none
Caller : general
=cut
sub update_failed_anchor {
my($self, $failed_anchor_hash_ref, $analysis_id_which_failed, $test_mlssid) = @_;
unless (defined $failed_anchor_hash_ref && defined $analysis_id_which_failed && defined $test_mlssid) {
throw("update_failed_anchor must have both a failed_anchor_id and the current analysis_id");
}
my $update = qq{
UPDATE anchor_align SET anchor_status = ? WHERE anchor_id = ? AND method_link_species_set_id = ?};
my $sth = $self->prepare($update);
foreach my $failed_anchor(%{$failed_anchor_hash_ref}) {
$sth->execute($analysis_id_which_failed, $failed_anchor, $test_mlssid) or die $self->errstr;
}
return 1;
}
=head2 fetch_all_dnafrag_ids
Arg[1] : listref of genome_db_ids
Example :
Description:
Returntype : arrayref
Exceptions : none
Caller : general
=cut
sub fetch_all_dnafrag_ids {
my($self, $mlssid) = @_;
my $return_hashref;
my $dnafrag_query = qq{
SELECT DISTINCT(aa.dnafrag_id), df.genome_db_id FROM anchor_align aa
INNER JOIN dnafrag df on aa.dnafrag_id = df.dnafrag_id
WHERE aa.method_link_species_set_id = ?};
# WHERE df.genome_db_id = ?};
my $sth = $self->prepare($dnafrag_query);
$sth->execute($mlssid);
while(my@row = $sth->fetchrow_array) {
push(@{$return_hashref->{$row[1]}}, $row[0]);
}
return $return_hashref;
}
=head2 fetch_all_anchors_by_genome_db_id_and_mlssid
Arg[0] : genome_db_id, string
Arg[1] : mlssid, string
Example :
Description:
Returntype : arrayref
Exceptions : none
Caller : general
=cut
#HACK
sub fetch_all_anchors_by_genome_db_id_and_mlssid {
my($self, $genome_db_id, $test_mlssid) = @_;
unless (defined $genome_db_id && defined $test_mlssid) {
throw("fetch_all_anchors_by_dnafrag_id_and_test_mlssid must
have a genome_db_id and a test_mlssid");
}
my $dnafrag_query = qq{
SELECT aa.dnafrag_id, aa.anchor_align_id, aa.anchor_id, aa.dnafrag_start, aa.dnafrag_end
FROM anchor_align aa
INNER JOIN dnafrag df ON df.dnafrag_id = aa.dnafrag_id
WHERE df.genome_db_id = ? AND aa.method_link_species_set_id = ? AND anchor_status
IS NULL ORDER BY dnafrag_start, dnafrag_end};
my $sth = $self->prepare($dnafrag_query);
$sth->execute($genome_db_id, $test_mlssid) or die $self->errstr;
return $sth->fetchall_arrayref();
}
=head2 fetch_all_anchors_by_dnafrag_id
Arg[1] : dnafrag_id, string
Example :
Description:
Returntype : arrayref
Exceptions : none
Caller : general
=cut
sub fetch_all_anchors_by_dnafrag_id_and_test_mlssid {
my($self, $dnafrag_id, $test_mlssid) = @_;
unless (defined $dnafrag_id && defined $test_mlssid) {
throw("fetch_all_anchors_by_dnafrag_id_and_test_mlssid must
have a dnafrag_id and a test_mlssid");
}
my $dnafrag_query = qq{
SELECT aa.anchor_align_id, aa.anchor_id, aa.dnafrag_start, aa.dnafrag_end FROM anchor_align aa
WHERE aa.dnafrag_id = ? AND aa.method_link_species_set_id = ? AND anchor_status
IS NULL ORDER BY dnafrag_start, dnafrag_end};
my $sth = $self->prepare($dnafrag_query);
$sth->execute($dnafrag_id, $test_mlssid) or die $self->errstr;
return $sth->fetchall_arrayref();
}
=head2 fetch_all_overlapping_anchors
Args : none
Example :
Description:
Returntype : none
Exceptions : none
Caller : general
=cut
sub fetch_all_filtered_anchors {
my($self) = @_;
my %Return_hash;
my $fetch_query = qq{
SELECT anchor_id, dnafrag_id, dnafrag_start, dnafrag_end, num_of_sequences, num_of_organisms
FROM anchor_align WHERE anchor_status IS NULL ORDER BY dnafrag_id, dnafrag_start, dnafrag_end};
my $sth = $self->prepare($fetch_query);
$sth->execute() or die $self->errstr;
my$array_ref = $sth->fetchall_arrayref();
for(my$i=0;$i<@{$array_ref};$i++) {
push(@{$Return_hash{$array_ref->[$i]->[1]}},
[ $array_ref->[$i]->[0], $array_ref->[$i]->[2], $array_ref->[$i]->[3], $array_ref->[$i]->[4], $array_ref->[$i]->[5] ]);
# [ anchor_id, dnafrag_start, dnafrag_end, num_of_seqs_that_hit_the_genomic_position, num_of_organisms_from_which_seqs_derived ]
splice(@{$array_ref}, $i, 1); #reduce momory used
$i--;
}
return \%Return_hash;
}
=head2 fetch_by_dbID
Arg [1] : int $dbID
Example :
Description: Returns the AnchorAlign obejcts with this anchor_align_id
Returntype : Bio::EnsEMBL::Compara::Production::AnchorAlign object
Exceptions :
Caller : general
=cut
sub fetch_by_dbID {
my ($self, $id) = @_;
unless (defined $id) {
throw("fetch_by_dbID must have an id");
}
my @tabs = $self->_tables;
my ($name, $syn) = @{$tabs[0]};
#construct a constraint like 't1.table1_id = 1'
my $constraint = "${syn}.${name}_id = $id";
#return first element of _generic_fetch list
my ($obj) = @{$self->_generic_fetch($constraint)};
return $obj;
}
=head2 fetch_all_by_MethodLinkSpeciesSet
Arg [1] : Bio::EnsEMBL::Compara::MethodLinkSpeciesSet $mlss
Example :
Description: Returns all the AnchorAlign obejcts for this MethodLinkSpeciesSet
Returntype : listref of Bio::EnsEMBL::Compara::Production::AnchorAlign objects
Exceptions :
Caller : general
=cut
sub fetch_all_by_MethodLinkSpeciesSet {
my ($self, $method_link_species_set) = @_;
unless (UNIVERSAL::isa($method_link_species_set, "Bio::EnsEMBL::Compara::MethodLinkSpeciesSet")) {
throw("[$method_link_species_set] must be a Bio::EnsEMBL::Compara::MethodLinkSpeciesSet object");
}
my @tabs = $self->_tables;
my ($name, $syn) = @{$tabs[0]};
#construct a constraint like 't1.table1_id = 1'
my $constraint = "aa.method_link_species_set_id = ". $method_link_species_set->dbID;
#return first element of _generic_fetch list
return $self->_generic_fetch($constraint);
}
############################
#
# INTERNAL METHODS
# (pseudo subclass methods)
#
############################
#internal method used in multiple calls above to build objects from table data
sub _tables {
my $self = shift;
return (['anchor_align', 'aa'] );
}
sub _columns {
my $self = shift;
return qw (aa.anchor_align_id
aa.method_link_species_set_id
aa.anchor_id
aa.dnafrag_id
aa.dnafrag_start
aa.dnafrag_end
aa.dnafrag_strand
aa.score
aa.num_of_organisms
aa.num_of_sequences
aa.anchor_status
);
}
sub _default_where_clause {
my $self = shift;
return '';
}
sub _final_clause {
my $self = shift;
$self->{'_final_clause'} = shift if(@_);
return $self->{'_final_clause'};
}
sub _objs_from_sth {
my ($self, $sth) = @_;
my %column;
$sth->bind_columns( \( @column{ @{$sth->{NAME_lc} } } ));
my $anchor_aligns = [];
while ($sth->fetch()) {
my $this_anchor_align;
$this_anchor_align = Bio::EnsEMBL::Compara::Production::AnchorAlign->new();
$this_anchor_align->adaptor($self);
$this_anchor_align->dbID($column{'anchor_align_id'});
$this_anchor_align->method_link_species_set_id($column{'method_link_species_set_id'});
$this_anchor_align->anchor_id($column{'anchor_id'});
$this_anchor_align->dnafrag_id($column{'dnafrag_id'});
$this_anchor_align->dnafrag_start($column{'dnafrag_start'});
$this_anchor_align->dnafrag_end($column{'dnafrag_end'});
$this_anchor_align->dnafrag_strand($column{'dnafrag_strand'});
$this_anchor_align->score($column{'score'});
$this_anchor_align->num_of_organisms($column{'num_of_organisms'});
$this_anchor_align->num_of_sequences($column{'num_of_sequences'});
$this_anchor_align->anchor_status($column{'anchor_status'});
push(@$anchor_aligns, $this_anchor_align);
}
$sth->finish;
return $anchor_aligns;
}
=head2 _generic_fetch
Arg [1] : (optional) string $constraint
An SQL query constraint (i.e. part of the WHERE clause)
Arg [2] : (optional) string $logic_name
the logic_name of the analysis of the features to obtain
Example : $fts = $a->_generic_fetch('contig_id in (1234, 1235)', 'Swall');
Description: Performs a database fetch and returns feature objects in
contig coordinates.
Returntype : listref of Bio::EnsEMBL::Production::DnaFragChunk in contig coordinates
Exceptions : none
Caller : internal
=cut
sub _generic_fetch {
my ($self, $constraint, $join) = @_;
my @tables = $self->_tables;
my $columns = join(', ', $self->_columns());
if ($join) {
foreach my $single_join (@{$join}) {
my ($tablename, $condition, $extra_columns) = @{$single_join};
if ($tablename && $condition) {
push @tables, $tablename;
if($constraint) {
$constraint .= " AND $condition";
} else {
$constraint = " $condition";
}
}
if ($extra_columns) {
$columns .= ", " . join(', ', @{$extra_columns});
}
}
}
#construct a nice table string like 'table1 t1, table2 t2'
my $tablenames = join(', ', map({ join(' ', @$_) } @tables));
my $sql = "SELECT $columns FROM $tablenames";
my $default_where = $self->_default_where_clause;
my $final_clause = $self->_final_clause;
#append a where clause if it was defined
if($constraint) {
$sql .= " WHERE $constraint ";
if($default_where) {
$sql .= " AND $default_where ";
}
} elsif($default_where) {
$sql .= " WHERE $default_where ";
}
#append additional clauses which may have been defined
$sql .= " $final_clause" if($final_clause);
my $sth = $self->prepare($sql);
$sth->execute;
# print STDERR "sql execute finished. about to build objects\n";
return $self->_objs_from_sth($sth);
}
1;
]]>