Bio::EnsEMBL::Compara::DBSQL
GenomicAlignAdaptor
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Summary
Bio::EnsEMBL::DBSQL::GenomicAlignAdaptor - Object adaptor to access data in the genomic_align table
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
Please, consider using the Bio::EnsEMBL::Compara::DBSQL::GenomicAlignBlockAdaptor instead.
use Bio::EnsEMBL::Registry;
my $reg = "Bio::EnsEMBL::Registry";
$reg->load_registry_from_db(
-host => "ensembldb.ensembl.org",
-user => "anonymous");
my $genomic_align_adaptor = $reg->get_adaptor(
"Multi", "compara", "GenomicAlign");
$genomic_align_adaptor->store($synteny_region);
my $genomic_align = $genomic_align_adaptor->fetch_by_dbID(1);
my $genomic_aligns = $genomic_align_adaptor->
fetch_by_GenomicAlignBlock($genomic_align_block);
my $genomic_aligns = $genomic_align_adaptor->
fetch_by_genomic_align_block_id(1001);
$genomic_align_adaptor->delete_by_genomic_align_block_id(1001);
$genomic_align = $genomic_align_adaptor->
retrieve_all_direct_attributes($genomic_align);
$genomic_align_adaptor->use_autoincrement(0);
Description
This module is intended to access data in the genomic_align table. In most cases, you want to use
the Bio::EnsEMBL::Compara::DBSQL::GenomicAlignBlockAdaptor instead.
Each alignment is represented by Bio::EnsEMBL::Compara::GenomicAlignBlock. Each GenomicAlignBlock
contains several Bio::EnsEMBL::Compara::GenomicAlign, one per sequence included in the alignment.
The GenomicAlign contains information about the coordinates of the sequence and the sequence of
gaps, information needed to rebuild the aligned sequence. By combining all the aligned sequences
of the GenomicAlignBlock, it is possible to get the orignal alignment back.
Methods
Methods description
Arg 1 : integer $genomic_align_block_id
Example : $gen_ali_blk_adaptor->delete_by_genomic_align_block_id(352158763);
Description: It removes the matching GenomicAlign objects from the database
Returntype : none
Exceptions : none
Caller : general
Status : Stable |
Arg 1 : Bio::EnsEMBL::Compara::GenomicAlignBlock object with a valid dbID
Example : my $genomic_aligns =
$genomic_align_adaptor->fetch_all_by_GenomicAlignBlock($genomic_align_block);
Description: Retrieve the corresponding
Bio::EnsEMBL::Compara::GenomicAlign objects
Returntype : ref. to an array of Bio::EnsEMBL::Compara::GenomicAlign objects
Exceptions : Returns a ref. to an empty array if there are no matching entries
Exceptions : Thrown if $genomic_align_block is not a
Bio::EnsEMBL::Compara::GenomicAlignBlock object
Caller : object::methodname
Status : Stable |
Arg 1 : integer $genomic_align_block_id
Example : my $genomic_aligns =
$genomic_align_adaptor->fetch_all_by_genomic_align_block_id(23134);
Description: Retrieve the corresponding
Bio::EnsEMBL::Compara::GenomicAlign objects
Returntype : ref. to an array of Bio::EnsEMBL::Compara::GenomicAlign objects
Exceptions : Returns a ref. to an empty array if there are no matching entries
Exceptions : Thrown if $genomic_align_block is neither a number
Caller : object::methodname
Status : Stable |
Arg 1 : integer $dbID
Example : my $genomic_align = $genomic_align_adaptor->fetch_by_dbID(23134);
Description: Retrieve the corresponding
Bio::EnsEMBL::Compara::GenomicAlign object
Returntype : Bio::EnsEMBL::Compara::GenomicAlign object
Exceptions : Returns undef if no matching entry is found in the database.
Caller : object::methodname
Status : Stable |
Arg [1] : list of args to super class constructor
Example : $ga_a = new Bio::EnsEMBL::Compara::GenomicAlignAdaptor($dbobj);
Description: Creates a new GenomicAlignAdaptor. This
class should be instantiated through the get method on the
DBAdaptor rather than calling this method directly.
Returntype : none
Exceptions : none
Caller : Bio::EnsEMBL::DBSQL::DBConnection
Status : Stable |
Arg 1 : Bio::EnsEMBL::Compara::GenomicAlign $genomic_align
Example : $genomic_align_adaptor->retrieve_all_direct_attributes($genomic_align)
Description: Retrieve the all the direct attibutes corresponding to the dbID of the
Bio::EnsEMBL::Compara::GenomicAlign object. It is used after lazy fetching
of the object for populating it when required.
Returntype : Bio::EnsEMBL::Compara::GenomicAlign object
Exceptions :
Caller : none
Status : Stable |
Arg 1 : listref Bio::EnsEMBL::Compara::GenomicAlign $ga
The things you want to store
Example : none
Description: It stores the given GA in the database. Attached
objects are not stored. Make sure you store them first.
Returntype : none
Exceptions : throw if the linked Bio::EnsEMBL::Compara::DnaFrag object or
the linked Bio::EnsEMBL::Compara::GenomicAlignBlock or
the linked Bio::EnsEMBL::Compara::MethodLinkSpeciesSet
are not in the database
Caller : $object->methodname
Status : Stable |
Arg 1 :
Example :
Description:
Returntype :
Exceptions :
Caller : |
[Arg 1] : (optional)int value
Example : $genomic_align_adaptor->use_autoincrement(0);
Description: Getter/setter for the _use_autoincrement flag. This flag
is used when storing new objects with no dbID in the
database. If the flag is ON (default), the adaptor will
let the DB set the dbID using the AUTO_INCREMENT ability.
If you unset the flag, then the adaptor will look for the
first available dbID after 10^10 times the
method_link_species_set_id.
Returntype : integer
Exceptions :
Caller : none
Status : Stable |
Methods code
sub delete_by_genomic_align_block_id
{ my ($self, $genomic_align_block_id) = @_;
my $genomic_align_sql =
qq{DELETE FROM genomic_align WHERE genomic_align_block_id = ?};
my $sth = $self->prepare($genomic_align_sql);
$sth->execute($genomic_align_block_id);} | sub fetch_all_by_GenomicAlignBlock
{ my ($self, $genomic_align_block) = @_;
my $genomic_aligns = [];
throw("$genomic_align_block is not a Bio::EnsEMBL::Compara::GenomicAlignBlock object")
if (!$genomic_align_block->isa("Bio::EnsEMBL::Compara::GenomicAlignBlock"));
my $genomic_align_block_id = $genomic_align_block->dbID;
return $self->fetch_all_by_genomic_align_block_id($genomic_align_block_id);} | sub fetch_all_by_genomic_align_block_id
{ my ($self, $genomic_align_block_id) = @_;
my $genomic_aligns = [];
my $sql = qq{
SELECT
genomic_align_id,
genomic_align_block_id,
method_link_species_set_id,
dnafrag_id,
dnafrag_start,
dnafrag_end,
dnafrag_strand,
cigar_line,
level_id
FROM
genomic_align
WHERE
genomic_align_block_id = ?
};
my $sth = $self->prepare($sql);
$sth->execute($genomic_align_block_id);
while (my @values = $sth->fetchrow_array()) {
my $this_genomic_align = new Bio::EnsEMBL::Compara::GenomicAlign(
-dbID => $values[0],
-adaptor => $self,
-genomic_align_block_id => $values[1],
-method_link_species_set_id => $values[2],
-dnafrag_id => $values[3],
-dnafrag_start => $values[4],
-dnafrag_end => $values[5],
-dnafrag_strand => $values[6],
-cigar_line => $values[7],
-level_id => $values[8],
);
push(@$genomic_aligns, $this_genomic_align);
}
return $genomic_aligns;} | sub fetch_by_dbID
{ my ($self, $dbID) = @_;
my $genomic_align;
my $sql = qq{
SELECT
genomic_align_id,
genomic_align_block_id,
method_link_species_set_id,
dnafrag_id,
dnafrag_start,
dnafrag_end,
dnafrag_strand,
cigar_line,
level_id
FROM
genomic_align
WHERE
genomic_align_id = ?
};
my $sth = $self->prepare($sql);
$sth->execute($dbID);
my @values = $sth->fetchrow_array();
$genomic_align = new Bio::EnsEMBL::Compara::GenomicAlign(
-dbID => $values[0],
-adaptor => $self,
-genomic_align_block_id => $values[1],
-method_link_species_set_id => $values[2],
-dnafrag_id => $values[3],
-dnafrag_start => $values[4],
-dnafrag_end => $values[5],
-dnafrag_strand => $values[6],
-cigar_line => $values[7],
-level_id => $values[8],
);
return $genomic_align;} | sub new
{ my $class = shift;
my $self = $class->SUPER::new(@_);
$self->{_use_autoincrement} = 1;
return $self;} | sub retrieve_all_direct_attributes
{ my ($self, $genomic_align) = @_;
my $sql = qq{
SELECT
genomic_align_block_id,
method_link_species_set_id,
dnafrag_id,
dnafrag_start,
dnafrag_end,
dnafrag_strand,
cigar_line,
level_id
FROM
genomic_align
WHERE
genomic_align_id = ?
};
my $sth = $self->prepare($sql);
$sth->execute($genomic_align->dbID);
my ($genomic_align_block_id, $method_link_species_set_id, $dnafrag_id, $dnafrag_start, $dnafrag_end,
$dnfrag_strand, $cigar_line, $level_id) = $sth->fetchrow_array();
$genomic_align->adaptor($self);
$genomic_align->genomic_align_block_id($genomic_align_block_id) if (defined($genomic_align_block_id));
$genomic_align->method_link_species_set_id($method_link_species_set_id) if (defined($method_link_species_set_id));
$genomic_align->dnafrag_id($dnafrag_id) if (defined($dnafrag_id));
$genomic_align->dnafrag_start($dnafrag_start) if (defined($dnafrag_start));
$genomic_align->dnafrag_end($dnafrag_end) if (defined($dnafrag_end));
$genomic_align->dnafrag_strand($dnfrag_strand) if (defined($dnfrag_strand));
$genomic_align->cigar_line($cigar_line) if (defined($cigar_line));
$genomic_align->level_id($level_id) if (defined($level_id));
return $genomic_align;} | sub store
{ my ( $self, $genomic_aligns ) = @_;
my $genomic_align_sql = qq{INSERT INTO genomic_align (
genomic_align_id,
genomic_align_block_id,
method_link_species_set_id,
dnafrag_id,
dnafrag_start,
dnafrag_end,
dnafrag_strand,
cigar_line,
level_id
) VALUES (?,?,?, ?,?,?, ?,?,?)};
my $genomic_align_sth = $self->prepare($genomic_align_sql);
for my $ga ( @$genomic_aligns ) {
if(!defined($ga->dnafrag) or !defined($ga->dnafrag->dbID)) {
throw( "dna_fragment in GenomicAlign is not in DB" );
}
if(!defined($ga->genomic_align_block) or !defined($ga->genomic_align_block->dbID)) {
throw( "genomic_align_block in GenomicAlign is not in DB" );
}
if(!defined($ga->method_link_species_set) or !defined($ga->method_link_species_set->dbID)) {
throw( "method_link_species_set in GenomicAlign is not in DB" );
}
my $lock_tables = 0;
if (!$ga->dbID and !$self->use_autoincrement()) {
$lock_tables = 1;
$self->dbc->do(qq{ LOCK TABLES genomic_align WRITE });
my $sql =
"SELECT MAX(genomic_align_id) FROM genomic_align WHERE".
" genomic_align_block_id > ".$ga->method_link_species_set->dbID.
"0000000000 AND genomic_align_block_id < ".
($ga->method_link_species_set->dbID + 1)."0000000000";
my $sth = $self->prepare($sql);
$sth->execute();
my $genomic_align_id = ($sth->fetchrow_array() or
($ga->method_link_species_set->dbID * 10000000000));
$ga->dbID($genomic_align_id + 1);
}
$genomic_align_sth->execute(
($ga->dbID or "NULL"),
$ga->genomic_align_block->dbID,
$ga->method_link_species_set->dbID,
$ga->dnafrag->dbID,
$ga->dnafrag_start,
$ga->dnafrag_end,
$ga->dnafrag_strand,
($ga->cigar_line or "NULL"),
($ga->level_id or 1)
);
if ($lock_tables) {
$self->dbc->do("UNLOCK TABLES");
}
if (!$ga->dbID) {
$ga->dbID($genomic_align_sth->{'mysql_insertid'});
}
info("Stored Bio::EnsEMBL::Compara::GenomicAlign ".
($ga->dbID or "NULL").
", gab=".$ga->genomic_align_block->dbID.
", mlss=".$ga->method_link_species_set->dbID.
", dnaf=".$ga->dnafrag->dbID.
" [".$ga->dnafrag_start.
"-".$ga->dnafrag_end."]".
" (".$ga->dnafrag_strand.")".
", cgr=".($ga->cigar_line or "NULL").
", lvl=".($ga->level_id or 1));
}} | sub store_daf
{ my ($self, $dafs, $dnafrag, $hdnafrag, $alignment_type) = @_;
my @gas;
foreach my $daf (@{$dafs}) {
my $ga = Bio::EnsEMBL::Compara::GenomicAlign->new_fast
('consensus_dnafrag' => $dnafrag,
'consensus_start' => $daf->start,
'consensus_end' => $daf->end,
'query_dnafrag' => $hdnafrag,
'query_start' => $daf->hstart,
'query_end' => $daf->hend,
'query_strand' => $daf->hstrand,
'alignment_type' => $alignment_type,
'score' => $daf->score,
'perc_id' => $daf->percent_id,
'group_id' => $daf->group_id,
'level_id' => $daf->level_id,
'cigar_line' => $daf->cigar_string
);
push @gas, $ga;
}
$self->store(\@gas);} | sub use_autoincrement
{ my ($self, $value) = @_;
if (defined $value) {
$self->{_use_autoincrement} = $value;
}
return $self->{_use_autoincrement};
}
1;} | General documentation
This class inherits all the methods and attributes from Bio::EnsEMBL::DBSQL::BaseAdaptor
- Bio::EnsEMBL::Registry
- Bio::EnsEMBL::DBSQL::BaseAdaptor
- Bio::EnsEMBL::Compara::DBSQL::GenomicAlignBlockAdaptor
- Bio::EnsEMBL::Compara::GenomicAlignBlock
- Bio::EnsEMBL::Compara::GenomicAlign
- Bio::EnsEMBL::Compara::DnaFrag;
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _