Raw content of Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::ImportAlignment
<![CDATA[#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
=pod
=head1 NAME
Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::ImportAlignment
=head1 SYNOPSIS
=head1 DESCRIPTION
This module imports a specified alignment. This is used in the low coverage genome alignment pipeline for importing the high coverage alignment which is used to build the low coverage genomes on.
=head1 PARAMETERS
=head1 CONTACT
Post questions to the Ensembl development list: ensembl-dev@ebi.ac.uk
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
package Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::ImportAlignment;
use strict;
use Bio::EnsEMBL::Registry;
use Bio::EnsEMBL::Compara::Production::DBSQL::DBAdaptor;
use Bio::EnsEMBL::Utils::Exception qw(throw);
use Bio::EnsEMBL::Compara::Graph::NewickParser;
use Bio::EnsEMBL::Hive::Process;
our @ISA = qw(Bio::EnsEMBL::Hive::Process);
=head2 fetch_input
Title : fetch_input
Usage : $self->fetch_input
Function: Fetches input data for gerp from the database
Returns : none
Args : none
=cut
sub fetch_input {
my( $self) = @_;
#create a Compara::DBAdaptor which shares the same DBI handle
#with $self->db (Hive DBAdaptor)
$self->{'comparaDBA'} = Bio::EnsEMBL::Compara::Production::DBSQL::DBAdaptor->new(-DBCONN=>$self->db->dbc);
$self->{'comparaDBA'}->dbc->disconnect_when_inactive(0);
$self->{'hiveDBA'} = Bio::EnsEMBL::Hive::DBSQL::DBAdaptor->new(-DBCONN => $self->{'comparaDBA'}->dbc);
#read from analysis table
$self->get_params($self->parameters);
#read from analysis_job table
$self->get_params($self->input_id);
my $reg = "Bio::EnsEMBL::Registry";
$reg->load_registry_from_url($self->from_db_url);
}
=head2 run
Title : run
Usage : $self->run
Function: Run gerp
Returns : none
Args : none
=cut
sub run {
my $self = shift;
$self->importAlignment();
}
=head2 write_output
Title : write_output
Usage : $self->write_output
Function: Write results to the database
Returns : 1
Args : none
=cut
sub write_output {
my ($self) = @_;
return 1;
}
#Uses copy_data method from copy_data.pl script
sub importAlignment {
my $self = shift;
#if the database name is defined in the url, then open that
if ($self->from_db_url =~ /mysql:\/\/.*@.*\/.+/) {
$self->{'from_comparaDBA'} = new Bio::EnsEMBL::Compara::DBSQL::DBAdaptor(-url=>$self->from_db_url);
} else {
#open the most recent compara database
$self->{'from_comparaDBA'} = Bio::EnsEMBL::Registry->get_DBAdaptor("Multi", "compara");
}
my $analysis = $self->db->get_AnalysisAdaptor->fetch_by_logic_name("ImportAlignment");
my $dbname = $self->{'from_comparaDBA'}->dbc->dbname;
my $analysis_id = $analysis->dbID;
my $mlss_id = $self->method_link_species_set_id;
#copy genomic_align_block table
copy_data($self->{'from_comparaDBA'}, $self->{'comparaDBA'},
"genomic_align_block",
"SELECT * FROM genomic_align_block WHERE method_link_species_set_id = $mlss_id");
my $do_all = 1;
if ($do_all) {
#copy genomic_align table
copy_data($self->{'from_comparaDBA'}, $self->{'comparaDBA'},
"genomic_align",
"SELECT ga.*".
" FROM genomic_align_block gab LEFT JOIN genomic_align ga USING (genomic_align_block_id)".
" WHERE gab.method_link_species_set_id = $mlss_id");
#copy genomic_align_group table
copy_data($self->{'from_comparaDBA'}, $self->{'comparaDBA'},
"genomic_align_group",
"SELECT gag.*".
" FROM genomic_align_block gab LEFT JOIN genomic_align ga USING (genomic_align_block_id)".
" LEFT JOIN genomic_align_group gag USING (genomic_align_id)".
" WHERE gag.group_id IS NOT NULL AND gab.method_link_species_set_id = $mlss_id");
#copy genomic_align_tree table
copy_data($self->{'from_comparaDBA'}, $self->{'comparaDBA'},
"genomic_align_tree",
"SELECT gat.*".
" FROM genomic_align_block gab LEFT JOIN genomic_align ga USING (genomic_align_block_id)".
" LEFT JOIN genomic_align_group gag USING (genomic_align_id)".
" LEFT JOIN genomic_align_tree gat ON (node_id=gag.group_id) WHERE gag.group_id IS NOT NULL AND gab.method_link_species_set_id = $mlss_id");
}
}
=head2 copy_data
Arg[1] : Bio::EnsEMBL::Compara::DBSQL::DBAdaptor $from_dba
Arg[2] : Bio::EnsEMBL::Compara::DBSQL::DBAdaptor $to_dba
Arg[3] : Bio::EnsEMBL::Compara::MethodLinkSpeciesSet $this_mlss
Arg[4] : string $table
Arg[5] : string $sql_query
Description : copy data in this table using this SQL query.
Returns :
Exceptions : throw if argument test fails
=cut
sub copy_data {
my ($from_dba, $to_dba, $table_name, $query) = @_;
print "Copying data in table $table_name\n";
my $sth = $from_dba->dbc->db_handle->column_info($from_dba->dbc->dbname, undef, $table_name, '%');
$sth->execute;
my $all_rows = $sth->fetchall_arrayref;
my $binary_mode = 0;
foreach my $this_col (@$all_rows) {
if (($this_col->[5] eq "BINARY") or ($this_col->[5] eq "VARBINARY") or
($this_col->[5] eq "BLOB") or ($this_col->[5] eq "BIT")) {
$binary_mode = 1;
last;
}
}
if ($binary_mode) {
#copy_data_in_binary_mode($from_dba, $to_dba, $table_name, $query);
} else {
copy_data_in_text_mode($from_dba, $to_dba, $table_name, $query);
}
}
=head2 copy_data_in_text_mode
Arg[1] : Bio::EnsEMBL::Compara::DBSQL::DBAdaptor $from_dba
Arg[2] : Bio::EnsEMBL::Compara::DBSQL::DBAdaptor $to_dba
Arg[3] : Bio::EnsEMBL::Compara::MethodLinkSpeciesSet $this_mlss
Arg[4] : string $table
Arg[5] : string $sql_query
Description : copy data in this table using this SQL query.
Returns :
Exceptions : throw if argument test fails
=cut
sub copy_data_in_text_mode {
my ($from_dba, $to_dba, $table_name, $query) = @_;
my $user = $to_dba->dbc->username;
my $pass = $to_dba->dbc->password;
my $host = $to_dba->dbc->host;
my $port = $to_dba->dbc->port;
my $dbname = $to_dba->dbc->dbname;
my $start = 0;
#my $step = 1000000;
my $step = 10000;
while (1) {
my $sth = $from_dba->dbc->prepare($query." LIMIT $start, $step");
$start += $step;
$sth->execute();
my $all_rows = $sth->fetchall_arrayref;
## EXIT CONDITION
return if (!@$all_rows);
my $filename = "/tmp/$table_name.copy_data.$$.txt";
open(TEMP, ">$filename") or die;
foreach my $this_row (@$all_rows) {
print TEMP join("\t", map {defined($_)?$_:'\N'} @$this_row), "\n";
}
close(TEMP);
if ($pass) {
system("mysqlimport", "-u$user", "-p$pass", "-h$host", "-P$port", "-L", "-l", "-i", $dbname, $filename);
} else {
system("mysqlimport", "-u$user", "-h$host", "-P$port", "-L", "-l", "-i", $dbname, $filename);
}
unlink("$filename");
}
}
#this assumes the from and to databases are on the same server.
sub importAlignment_old {
my $self = shift;
#if the database name is defined in the url, then open that
if ($self->from_db_url =~ /mysql:\/\/.*@.*\/.+/) {
$self->{'from_comparaDBA'} = new Bio::EnsEMBL::Compara::DBSQL::DBAdaptor(-url=>$self->from_db_url);
} else {
#open the most recent compara database
$self->{'from_comparaDBA'} = Bio::EnsEMBL::Registry->get_DBAdaptor("Multi", "compara");
}
my $analysis = $self->db->get_AnalysisAdaptor->fetch_by_logic_name("ImportAlignment");
my $dbname = $self->{'from_comparaDBA'}->dbc->dbname;
my $analysis_id = $analysis->dbID;
my $mlss_id = $self->method_link_species_set_id;
my $sql = "INSERT INTO genomic_align_block SELECT * FROM ?.genomic_align_block WHERE method_link_species_set_id = ?\n";
my $sth = $self->{'comparaDBA'}->dbc->prepare($sql);
$sth->execute($dbname, $mlss_id);
$sth->finish();
$sql = "INSERT INTO genomic_align SELECT genomic_align.* FROM ?.genomic_align LEFT JOIN WHERE method_link_species_set_id = ?\n";
my $sth = $self->{'comparaDBA'}->dbc->prepare($sql);
$sth->execute($dbname, $mlss_id);
$sth->finish();
$sql = "INSERT INTO genomic_align_group SELECT genomic_align_group.* FROM ?.genomic_align_group LEFT JOIN ?.genomic_align USING (genomic_align_id) LEFT JOIN ?.genomic_align_block USING (genomic_align_block_id) WHERE genomic_align_block.method_link_species_set_id = ?\n";
my $sth = $self->{'comparaDBA'}->dbc->prepare($sql);
$sth->execute($dbname, $dbname, $mlss_id);
$sth->finish();
$sql = "INSERT INTO genomic_align_tree SELECT genomic_align_tree.* FROM ?.genomic_align_tree LEFT JOIN ?.genomic_align_group ON (node_id=group_id) LEFT JOIN ?.genomic_align USING (genomic_align_id) LEFT JOIN ?.genomic_align_block WHERE genomic_align_block.method_link_species_set_id = ?\n";
my $sth = $self->{'comparaDBA'}->dbc->prepare($sql);
$sth->execute($dbname, $dbname, $dbname, $dbname, $mlss_id);
$sth->finish();
}
##########################################
#
# getter/setter methods
#
##########################################
sub method_link_species_set_id {
my $self = shift;
$self->{'_method_link_species_set_id'} = shift if(@_);
return $self->{'_method_link_species_set_id'};
}
sub from_db_url {
my $self = shift;
$self->{'_from_db_url'} = shift if(@_);
return $self->{'_from_db_url'};
}
##########################################
#
# internal methods
#
##########################################
sub get_params {
my $self = shift;
my $param_string = shift;
return unless($param_string);
print("parsing parameter string : ",$param_string,"\n");
my $params = eval($param_string);
return unless($params);
if(defined($params->{'method_link_species_set_id'})) {
$self->method_link_species_set_id($params->{'method_link_species_set_id'});
}
if (defined($params->{'from_db_url'})) {
$self->from_db_url($params->{'from_db_url'});
}
return 1;
}
]]>