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Summary

Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::ImportAlignment

Package variables

Included modules

Inherit

Bio::EnsEMBL::Hive::Process

Synopsis

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.

Methods

Methods description

  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

  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

    Title   :   fetch_input
    Usage   :   $self->fetch_input
    Function:   Fetches input data for gerp from the database
    Returns :   none
    Args    :   none

    Title   :   run
    Usage   :   $self->run
    Function:   Run gerp
    Returns :   none
    Args    :   none

    Title   :   write_output
    Usage   :   $self->write_output
    Function:   Write results to the database
    Returns :   1
    Args    :   none

Methods code

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);
  }

}

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 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);

}

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;

}

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");
}

}

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 run {

    my $self = shift;
    $self->importAlignment();

}

sub write_output {

    my ($self) = @_;

    return 1;
}

#Uses copy_data method from copy_data.pl script

}

General documentation

Post questions to the Ensembl development list: ensembl-dev@ebi.ac.uk

The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _