The London Perl and Raku Workshop takes place on 26th Oct 2024. If your company depends on Perl, please consider sponsoring and/or attending.
 / 
Bio-EnsEMBL-112.0.0_57
River stage zero No dependents
/ Bio::EnsEMBL::DBSQL::CoordSystemAdaptor

LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

     http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

CONTACT

  Please email comments or questions to the public Ensembl
  developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.

  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     : Stable

fetch_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     : Stable

fetch_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     : Stable

fetch_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     : Stable

fetch_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     : Stable

fetch_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     : Stable

fetch_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     : Stable

fetch_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     : Stable

fetch_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     : Stable

get_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     : Stable

get_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     : Stable

get_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     : Stable

store_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     : Experimental

store_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     : Experimental

fetch_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     : Stable

fetch_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     : Stable

store

  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     : Stable

remove

  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