Bio::EnsEMBL::Compara::DBSQL AnchorAlignAdaptor
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Summary
Bio::EnsEMBL::Compara::Production::DBSQL::AnchorAlignAdaptor
Package variables
No package variables defined.
Included modules
Bio::EnsEMBL::Compara::Production::EPOanchors::AnchorAlign
Bio::EnsEMBL::DBSQL::BaseAdaptor
Bio::EnsEMBL::Hive::DBSQL::AnalysisDataAdaptor
Bio::EnsEMBL::Utils::Exception qw ( throw warning )
Data::Dumper
Inherit
Bio::EnsEMBL::DBSQL::BaseAdaptor
Synopsis
Description
No description!
Methods
_columns
No description
Code
_default_where_clause
No description
Code
_final_clause
No description
Code
_generic_fetchDescriptionCode
_objs_from_sth
No description
Code
_tables
No description
Code
fetch_all_anchor_ids_by_test_mlssid_and_genome_db_idsDescriptionCode
fetch_all_anchors_by_dnafrag_id_and_test_mlssid
No description
Code
fetch_all_anchors_by_genome_db_id_and_mlssidDescriptionCode
fetch_all_anchors_with_zero_strandDescriptionCode
fetch_all_by_MethodLinkSpeciesSetDescriptionCode
fetch_all_by_anchor_id_and_mlss_idDescriptionCode
fetch_all_dnafrag_idsDescriptionCode
fetch_all_filtered_anchors
No description
Code
fetch_anchors_by_genomedb_idDescriptionCode
fetch_by_dbIDDescriptionCode
fetch_dnafrag_and_genome_db_ids_by_test_mlssidDescriptionCode
fetch_dnafrag_idDescriptionCode
get_target_file
No description
Code
storeDescriptionCode
store_exonerate_hits
No description
Code
update_failed_anchorDescriptionCode
update_zero_strand_anchorsDescriptionCode
Methods description
_generic_fetchcode    nextTop
  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
fetch_all_anchor_ids_by_test_mlssid_and_genome_db_idscodeprevnextTop
  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
fetch_all_anchors_by_genome_db_id_and_mlssid codeprevnextTop
  Arg[0]     : genome_db_id, string
Arg[1] : mlssid, string
Example :
Description:
Returntype : arrayref
Exceptions : none
Caller : general
fetch_all_anchors_with_zero_strandcodeprevnextTop
  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
fetch_all_by_MethodLinkSpeciesSetcodeprevnextTop
  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
fetch_all_by_anchor_id_and_mlss_idcodeprevnextTop
  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
fetch_all_dnafrag_ids codeprevnextTop
  Arg[1]     : listref of genome_db_ids 
Example :
Description:
Returntype : arrayref
Exceptions : none
Caller : general
fetch_anchors_by_genomedb_idcodeprevnextTop
  Arg[1]     : 
Arg[2] :
Example :
Description:
Returntype :
Exceptions : none
Caller : general
fetch_by_dbIDcodeprevnextTop
  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
fetch_dnafrag_and_genome_db_ids_by_test_mlssidcodeprevnextTop
  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
fetch_dnafrag_idcodeprevnextTop
  Arg[1]     : 
Arg[2] :
Example :
Description:
Returntype :
Exceptions : none
Caller : general
storecodeprevnextTop
  Arg[1]     : one or many DnaFragChunk objects
Example : $adaptor->store($chunk);
Description: stores DnaFragChunk objects into compara database
Returntype : none
Exceptions : none
Caller : general
update_failed_anchorcodeprevnextTop
  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
update_zero_strand_anchorscodeprevnextTop
  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
Methods code
_columnsdescriptionprevnextTop
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
            );
}
_default_where_clausedescriptionprevnextTop
sub _default_where_clause {
  my $self = shift;
  return '';
}
_final_clausedescriptionprevnextTop
sub _final_clause {
  my $self = shift;
  $self->{'_final_clause'} = shift if(@_);
  return $self->{'_final_clause'};
}
_generic_fetchdescriptionprevnextTop
sub _generic_fetch {
  my ($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;
}
_objs_from_sthdescriptionprevnextTop
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;
}
_tablesdescriptionprevnextTop
sub _tables {
  my $self = shift;

  return (['anchor_align', 'aa'] );
}
fetch_all_anchor_ids_by_test_mlssid_and_genome_db_idsdescriptionprevnextTop
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 $sth->fetchall_arrayref;
}
fetch_all_anchors_by_dnafrag_id_and_test_mlssiddescriptionprevnextTop
sub fetch_all_anchors_by_dnafrag_id_and_test_mlssid {
	my($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 $sth->fetchall_arrayref();
}
fetch_all_anchors_by_genome_db_id_and_mlssiddescriptionprevnextTop
sub fetch_all_anchors_by_genome_db_id_and_mlssid {
	my($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 $sth->fetchall_arrayref();
}
fetch_all_anchors_with_zero_stranddescriptionprevnextTop
sub fetch_all_anchors_with_zero_strand {
	my ($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 $sth->fetchall_arrayref;
}
fetch_all_by_MethodLinkSpeciesSetdescriptionprevnextTop
sub fetch_all_by_MethodLinkSpeciesSet {
  my ($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
}
fetch_all_by_anchor_id_and_mlss_iddescriptionprevnextTop
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 $sth->fetchall_hashref("anchor_align_id");
}
fetch_all_dnafrag_idsdescriptionprevnextTop
sub fetch_all_dnafrag_ids {
	my($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 $return_hashref;
}
fetch_all_filtered_anchorsdescriptionprevnextTop
sub fetch_all_filtered_anchors {
	my($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
$i--; } return\% Return_hash;
}
fetch_anchors_by_genomedb_iddescriptionprevnextTop
sub fetch_anchors_by_genomedb_id {
	my ($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 $return_hashref;
}
fetch_by_dbIDdescriptionprevnextTop
sub fetch_by_dbID {
  my ($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 $obj;
}
fetch_dnafrag_and_genome_db_ids_by_test_mlssiddescriptionprevnextTop
sub fetch_dnafrag_and_genome_db_ids_by_test_mlssid {
	my ($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;
}
fetch_dnafrag_iddescriptionprevnextTop
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];
	}
}


##########################
}
get_target_filedescriptionprevnextTop
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};
}
storedescriptionprevnextTop
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;
}
store_exonerate_hitsdescriptionprevnextTop
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;
}
update_failed_anchordescriptionprevnextTop
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 $self->errstr;
	}
	return 1;
}
update_zero_strand_anchorsdescriptionprevnextTop
sub update_zero_strand_anchors {
	my ($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;
	}
}
General documentation
CONTACTTop
Jessica Severin : jessica@ebi.ac.uk
APPENDIXTop
store_new_method_link_species_set_idTop
  Arg[1]     : 
Example :
Description:
Returntype : none
Exceptions : none
Caller : general
fetch_all_anchors_by_dnafrag_id Top
  Arg[1]     : dnafrag_id, string
Example :
Description:
Returntype : arrayref
Exceptions : none
Caller : general
fetch_all_overlapping_anchorsTop
  Args       : none
Example :
Description:
Returntype : none
Exceptions : none
Caller : general