Raw content of Bio::EnsEMBL::Pipeline::Tools::MM_Taxonomy
<![CDATA[package Bio::EnsEMBL::Pipeline::Tools::MM_Taxonomy;
use strict;
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use DBI;
# Use this module to fetch information from the Mole&Mushroom taxonomy tree
sub new {
my ( $class, @args ) = @_;
my $self = bless {}, $class;
my ( $mm_host , $mm_port , $mm_user, $mm_name ) = rearrange(
[ 'MM_HOST', 'MM_PORT','MM_USER', 'MM_NAME' ], @args );
$self->mm_host($mm_host || 'cbi3');
$self->mm_port($mm_port || 3306);
$self->mm_user($mm_user || 'genero');
$self->mm_name($mm_name || 'mm_ini');
$self->init_connection();
return $self;
}
sub init_connection {
my ( $self ) = @_;
my $dsn_mm_ini = "DBI:mysql:host=".$self->mm_host.":".$self->mm_name;
my $dbh_mm_ini = DBI->connect( $dsn_mm_ini, $self->mm_user, '',{ 'RaiseError' => 1 } );
my $mushroom_db;
my $query = "SELECT database_name FROM ini
WHERE database_category = 'mushroom'
AND current = 'yes'
AND available = 'yes'";
my $ini_sth = $dbh_mm_ini->prepare($query);
$ini_sth->execute() or die "Couldn't execute statement: " . $ini_sth->errstr;
while(my $hash = $ini_sth->fetchrow_hashref()) {
$mushroom_db = $hash->{'database_name'};
}
$ini_sth->finish();
my $dsn_mushroom = "DBI:mysql:host=".$self->mm_host.":$mushroom_db";
my $dbh_mushroom = DBI->connect( $dsn_mushroom, $self->mm_user, '',{ 'RaiseError' => 1 } );
$self->dbh($dbh_mushroom);
}
sub get_parent_id {
my ( $self, $taxon_id ) = @_;
my $sql = ' SELECT parent_id
FROM taxonomy
WHERE ncbi_tax_id=? ';
my $sth = $self->dbh->prepare($sql);
$sth->execute($taxon_id) or die "Couldn't execute statement: " . $sth->errstr;;
my ($parent_id) = $sth->fetchrow_array();
return $parent_id;
}
# Get all taxon id upstream of the given node id
sub get_all_parent_id {
my ( $self, $taxon_id ) = @_;
my $ids = [];
while(my $id = $self->get_parent_id($taxon_id)) {
push @$ids, $id;
$taxon_id = $id;
}
return $ids;
}
sub get_children_id {
my ( $self, $taxon_id ) = @_;
my $ids = [];
my $sql =' SELECT ncbi_tax_id
FROM taxonomy
WHERE parent_id=? ';
my $sth = $self->dbh->prepare($sql);
$sth->execute($taxon_id) or die "Couldn't execute statement: " . $sth->errstr;;
while (my ($id) = $sth->fetchrow_array()) { push @$ids, $id };
return $ids;
}
# Get all taxon id downstream of the given node id
sub get_all_children_id {
my ( $self, $taxon_id ) = @_;
my $ids = [];
for my $id (@{$self->get_children_id($taxon_id)}) {
push @$ids, $id;
push @$ids, @{$self->get_all_children_id($id)};
}
return $ids;
}
# this method does the same thing in a single query but is slower
sub get_all_children {
my ( $self, $taxon_id ) = @_;
my $ids = [];
my $sql =' SELECT t.ncbi_tax_id
FROM taxonomy p, taxonomy t
WHERE p.ncbi_tax_id = ?
AND p.lft < t.lft
AND p.rgt > t.rgt';
my $sth = $self->dbh->prepare($sql);
$sth->execute($taxon_id) or die "Couldn't execute statement: " . $sth->errstr;;
while (my ($id) = $sth->fetchrow_array()) { push @$ids, $id };
return $ids;
}
sub get_taxon_id {
my ( $self, $taxon_id ) = @_;
my $sql = ' SELECT n.name, t.rank, t.parent_id
FROM taxonomy_name n, taxonomy t
WHERE t.ncbi_tax_id= ?
AND n.name_type="scientific name"
AND n.ncbi_tax_id = t.ncbi_tax_id;';
my $sth = $self->dbh->prepare($sql);
$sth->execute($taxon_id) or die "Couldn't execute statement: " . $sth->errstr;;
my $hash = $sth->fetchrow_hashref();
return $hash;
}
sub print_taxon {
my ( $self, $tax_arr ) = @_;
print STDOUT "name\trank\tparent_id\n" if @$tax_arr;
for (@$tax_arr) {
my $hash = $self->get_taxon_id($_);
print STDOUT $hash->{name}."\t".$hash->{rank}."\t".$hash->{parent_id}."\n";
}
}
sub dbh {
my ( $self, $dbh ) = @_;
if ($dbh) {
$self->{'_dbh'} = $dbh;
}
return $self->{'_dbh'};
}
sub mm_name {
my ( $self, $mm_name ) = @_;
if ($mm_name) {
$self->{'_mm_name'} = $mm_name;
}
return $self->{'_mm_name'};
}
sub mm_host {
my ( $self, $mm_host ) = @_;
if ($mm_host) {
$self->{'_mm_host'} = $mm_host;
}
return $self->{'_mm_host'};
}
sub mm_port {
my ( $self, $mm_port ) = @_;
if ($mm_port) {
$self->{'_mm_port'} = $mm_port;
}
return $self->{'_mm_port'};
}
sub mm_user {
my ( $self, $mm_user ) = @_;
if ($mm_user) {
$self->{'_mm_user'} = $mm_user;
}
return $self->{'_mm_user'};
}
1;
]]>