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Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute
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Questions may also be sent to the Ensembl help desk at
<http://www.ensembl.org/Help/Contact>.NAME
Bio::EnsEMBL::DBSQL::CoordSystemAdaptor
SYNOPSIS
use Bio::EnsEMBL::Registry;
Bio::EnsEMBL::Registry->load_registry_from_db(
-host => 'ensembldb.ensembl.org',
-user => 'anonymous'
);
$csa = Bio::EnsEMBL::Registry->get_adaptor( "human", "core",
"coordsystem" );
#
# Get all coord systems in the database:
#
foreach my $cs ( @{ $csa->fetch_all() } ) {
print $cs->name, ' ', $cs->version, "\n";
}
#
# Fetching by name:
#
# use the default version of coord_system 'chromosome' (e.g. NCBI33):
$cs = $csa->fetch_by_name('chromosome');
# get an explicit version of coord_system 'chromosome':
$cs = $csa->fetch_by_name( 'chromsome', 'NCBI34' );
# get all coord_systems of name 'chromosome':
foreach $cs ( @{ $csa->fetch_all_by_name('chromosome') } ) {
print $cs->name, ' ', $cs->version, "\n";
}
#
# Fetching by rank:
#
$cs = $csa->fetch_by_rank(2);
#
# Fetching the pseudo coord system 'toplevel'
#
# Get the default top_level coord system:
$cs = $csa->fetch_top_level();
# can also use an alias in fetch_by_name:
$cs = $csa->fetch_by_name('toplevel');
# can also request toplevel using rank=0
$cs = $csa->fetch_by_rank(0);
#
# Fetching by sequence level:
#
# Get the coord system which is used to store sequence:
$cs = $csa->fetch_sequence_level();
# can also use an alias in fetch_by_name:
$cs = $csa->fetch_by_name('seqlevel');
#
# Fetching by id
#
$cs = $csa->fetch_by_dbID(1);DESCRIPTION
This adaptor allows the querying of information from the coordinate system adaptor.
Note that many coordinate systems do not have a concept of a version for the entire coordinate system (though they may have a per-sequence version). The 'chromosome' coordinate system usually has a version (i.e. the assembly version) but the clonal coordinate system does not (despite having individual sequence versions). In the case where a coordinate system does not have a version an empty string ('') is used instead.
METHODS
new
Arg [1] : See BaseAdaptor for arguments (none specific to this
subclass)
Example : $cs = $db->get_CoordSystemAdaptor(); #better than new()
Description: Creates a new CoordSystem adaptor and caches the contents
of the coord_system table in memory.
Returntype : Bio::EnsEMBL::DBSQL::CoordSystemAdaptor
Exceptions : none
Caller :
Status : Stablefetch_all
Arg [1] : none
Example : foreach my $cs (@{$csa->fetch_all()}) {
print $cs->name(), ' ', $cs->version(), "\n";
}
Description: Retrieves every coordinate system defined in the DB.
These will be returned in ascending order of rank. I.e.
The highest coordinate system with rank=1 would be first in the
array.
Returntype : listref of Bio::EnsEMBL::CoordSystems
Exceptions : none
Caller : general
Status : Stablefetch_by_rank
Arg [1] : int $rank
Example : my $cs = $coord_sys_adaptor->fetch_by_rank(1);
Description: Retrieves a CoordinateSystem via its rank. 0 is a special
rank reserved for the pseudo coordinate system 'toplevel'.
undef is returned if no coordinate system of the specified rank
exists.
Returntype : Bio::EnsEMBL::CoordSystem
Exceptions : none
Caller : general
Status : Stablefetch_by_name
Arg [1] : string $name
The name of the coordinate system to retrieve. Alternatively
this may be an alias for a real coordinate system. Valid
aliases are 'toplevel' and 'seqlevel'.
Arg [2] : string $version (optional)
The version of the coordinate system to retrieve. If not
specified the default version will be used.
Example : $coord_sys = $csa->fetch_by_name('clone');
$coord_sys = $csa->fetch_by_name('chromosome', 'NCBI33');
# toplevel is an pseudo coord system representing the highest
# coord system in a given region
# such as the chromosome coordinate system
$coord_sys = $csa->fetch_by_name('toplevel');
#seqlevel is an alias for the sequence level coordinate system
#such as the clone or contig coordinate system
$coord_sys = $csa->fetch_by_name('seqlevel');
Description: Retrieves a coordinate system by its name
Returntype : Bio::EnsEMBL::CoordSystem
Exceptions : throw if no name argument provided
warning if no version provided and default does not exist
Caller : general
Status : Stablefetch_all_by_name
Arg [1] : string $name
The name of the coordinate system to retrieve. This can be
the name of an actual coordinate system or an alias for a
coordinate system. Valid aliases are 'toplevel' and 'seqlevel'.
Example : foreach my $cs (@{$csa->fetch_all_by_name('chromosome')}){
print $cs->name(), ' ', $cs->version();
}
Description: Retrieves all coordinate systems of a particular name
Returntype : listref of Bio::EnsEMBL::CoordSystem objects
Exceptions : throw if no name argument provided
Caller : general
Status : Stablefetch_all_by_version
Arg [1] : string $version
The version of the coordinate systems to retrieve.
Example : foreach my $cs (@{$csa->fetch_all_by_version('GRCh37')}){
print $cs->name(), ' ', $cs->version();
}
Description: Retrieves all coordinate systems of a particular version
Returntype : ArrayRef of Bio::EnsEMBL::CoordSystem objects
Exceptions : throw if no name argument provided
Caller : general
Status : Stablefetch_by_dbID
Arg [1] : int dbID
Example : $cs = $csa->fetch_by_dbID(4);
Description: Retrieves a coord_system via its internal
identifier, or undef if no coordinate system with the provided
id exists.
Returntype : Bio::EnsEMBL::CoordSystem or undef
Exceptions : thrown if no coord_system exists for specified dbID
Caller : general
Status : Stablefetch_top_level
Arg [1] : none
Example : $cs = $csa->fetch_top_level();
Description: Retrieves the toplevel pseudo coordinate system.
Returntype : Bio::EnsEMBL::CoordSystem object
Exceptions : none
Caller : general
Status : Stablefetch_sequence_level
Arg [1] : none
Example : ($id, $name, $version) = $csa->fetch_sequence_level();
Description: Retrieves the coordinate system at which sequence
is stored at.
Returntype : Bio::EnsEMBL::CoordSystem
Exceptions : throw if no sequence_level coord system exists at all
throw if multiple sequence_level coord systems exists
Caller : general
Status : Stableget_default_version
Arg [1] : none
Example : $version = $csa->get_default_version();
Description: Retrieves the default version of the assembly
Returntype : String
Exceptions : throw if no default version is defined
Caller : general
Status : Stableget_all_versions
Arg [1] : none
Example : @versions = $csa->get_all_versions();
Description: Retrieves all the available versions of assemblies
Returntype : Listref of versions (strings)
Exceptions : throw if no version is defined
Caller : general
Status : Stableget_mapping_path
Arg [1] : Bio::EnsEMBL::CoordSystem $cs1
Arg [2] : Bio::EnsEMBL::CoordSystem $cs2
Example : foreach my $cs @{$csa->get_mapping_path($cs1,$cs2);
Description: Given two coordinate systems this will return a mapping path
between them if one has been defined. Allowed Mapping paths are
explicitly defined in the meta table. The following is an
example:
mysql> select * from meta where meta_key = 'assembly.mapping';
+---------+------------------+--------------------------------------+
| meta_id | meta_key | meta_value |
+---------+------------------+--------------------------------------+
| 20 | assembly.mapping | chromosome:NCBI34|contig |
| 21 | assembly.mapping | clone|contig |
| 22 | assembly.mapping | supercontig|contig |
| 23 | assembly.mapping | chromosome:NCBI34|contig|clone |
| 24 | assembly.mapping | chromosome:NCBI34|contig|supercontig |
| 25 | assembly.mapping | supercontig|contig|clone |
+---------+------------------+--------------------------------------+
For a one-step mapping path to be valid there needs to be
a relationship between the two coordinate systems defined in
the assembly table. Two step mapping paths work by building
on the one-step mapping paths which are already defined.
The first coordinate system in a one step mapping path must
be the assembled coordinate system and the second must be
the component.
Example of use:
my $cs1 = $cs_adaptor->fetch_by_name('contig');
my $cs2 = $cs_adaptor->fetch_by_name('chromosome');
my @path = @{$cs_adaptor->get_mapping_path($cs1,$cs2)};
if(!@path) {
print "No mapping path.";
}
elsif(@path == 2) {
print "2 step mapping path.";
print "Assembled = " . $path[0]->name() . "\n";
print "Component = " . $path[1]->name() . "\n";
} else {
print "Multi step mapping path\n";
}
Returntype : reference to a list of Bio::EnsEMBL::CoordSystem objects
Exceptions : none
Caller : general
Status : Stablestore_mapping_path
Arg [1] : Bio::EnsEMBL::CoordSystem $cs1
Arg [2] : Bio::EnsEMBL::CoordSystem $cs2
Arg [3..n] : Bio::EnsEMBL::CoordSystem $cs3..$csN
Example : my $pathref = $csa->store_mapping_path($cs1,$cs2);
Description: Given two or more coordinate systems this will store
mapping paths between them in the database.
For example, if $cs1 represents chrs of version
V1, $cs2 represents contigs, and $cs3 clones then, unless
they already exist, the following entries will be created
in the meta table;
+------------------+---------------------+
| meta_key | meta_value |
+------------------+---------------------+
| assembly.mapping | chr:V1|clone |
| assembly.mapping | clone|contig |
| assembly.mapping | chr:V1|clone|contig |
+------------------+---------------------+
For a one-step mapping path to be valid there needs to be
a relationship between the two coordinate systems defined in
the assembly table. Two step mapping paths work by building
on the one-step mapping paths which are already defined.
The first coordinate system in a one step mapping path must
be the assembled coordinate system and the second must be
the component.
Returntype : reference to a list of lists of new meta_value mapping strings
created for assembly.mapping
Exceptions : CoordSystems with no rank/duplicated rank
Caller : general
Status : Experimentalstore_multiple_mapping_path
Arg [1] : Bio::EnsEMBL::CoordSystem $cs1
Arg [2] : Bio::EnsEMBL::CoordSystem $cs2
Arg [3..n] : Bio::EnsEMBL::CoordSystem $cs3..$csN
Example : my $pathref = $csa->store_multiple_mapping_path($cs1,$cs2);
Description: Given two or more coordinate systems this will store
multiple mapping paths between them in the database.
Works similarly to the store_mapping_path method
But will presume every coord system can be mapped in multiple
ways to the other coord systems
This is represented by the use of '#' instead of '|'
in the mapping key
Returntype : reference to a list of lists of new meta_value mapping strings
created for assembly.mapping
Exceptions : CoordSystems with no rank/duplicated rank
Caller : general
Status : Experimentalfetch_by_attrib
Arg [1] : string attrib
Arg [2] : (optional) string version
Example : $csa->fetch_by_attrib('default_version','NCBIM37');
Description: Retrieves a CoordSystem object from the database that have the specified
attrib and version, if no version is specified, returns the default version
Returntype : Bio::EnsEMBL::CoordSystem object
Exceptions : throw when attrib not present
Caller : general
Status : Stablefetch_all_by_attrib
Arg [1] : string attrib
Example : $csa->fetch_all_by_attrib('default_version');
Description: Retrieves all CoordSystem object from the database that have the specified
attrib.
Returntype : reference to a list of Bio::EnsEMBL::CoordSystem objects
Exceptions : throw when attrib not present
Caller : general
Status : Stablestore
Arg [1] : Bio::EnsEMBL::CoordSystem
Example : $csa->store($coord_system);
Description: Stores a CoordSystem object in the database.
Returntype : none
Exceptions : Warning if CoordSystem is already stored in this database.
Caller : none
Status : Stableremove
Arg [1] : Bio::EnsEMBL::CoordSystem
Example : $csa->remove($coord_system);
Description: Removes a CoordSystem object from the database.
Returntype : none
Exceptions : Warning if CoordSystem is not stored in this database.
Caller : none
Status : Stable