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Bio-EnsEMBL-112.0_53
River stage zero No dependents
/ Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor

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.

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NAME

Bio::EnsEMBL::ArchiveStableIdAdaptor

SYNOPSIS

my $registry = "Bio::EnsEMBL::Registry";

my $archiveStableIdAdaptor =
  $registry->get_adaptor( 'Human', 'Core', 'ArchiveStableId' );

my $stable_id = 'ENSG00000068990';

my $arch_id = $archiveStableIdAdaptor->fetch_by_stable_id($stable_id);

print("Latest incarnation of this stable ID:\n");
printf( "  Stable ID: %s.%d\n",
  $arch_id->stable_id(), $arch_id->version() );
print("  Release: "
    . $arch_id->release() . " ("
    . $arch_id->assembly() . ", "
    . $arch_id->db_name()
    . ")\n" );

print "\nStable ID history:\n\n";

my $history =
  $archiveStableIdAdaptor->fetch_history_tree_by_stable_id(
  $stable_id);

foreach my $a ( @{ $history->get_all_ArchiveStableIds } ) {
  printf( "  Stable ID: %s.%d\n", $a->stable_id(), $a->version() );
  print("  Release: "
      . $a->release() . " ("
      . $a->assembly() . ", "
      . $a->db_name()
      . ")\n\n" );
}

DESCRIPTION

ArchiveStableIdAdaptor does all SQL to create ArchiveStableIds and works of

stable_id_event
mapping_session
peptite_archive
gene_archive

tables inside the core database.

This whole module has a status of At Risk as it is under development.

METHODS

fetch_by_stable_id
fetch_by_stable_id_version
fetch_by_stable_id_dbname
fetch_all_by_archive_id
fetch_predecessors_by_archive_id
fetch_successors_by_archive_id
fetch_history_tree_by_stable_id
add_all_current_to_history
list_dbnames
previous_dbname
next_dbname
get_peptide
get_current_release
get_current_assembly

RELATED MODULES

Bio::EnsEMBL::ArchiveStableId
Bio::EnsEMBL::StableIdEvent
Bio::EnsEMBL::StableIdHistoryTree

METHODS

fetch_by_stable_id

Arg [1]     : string $stable_id
Arg [2]     : (optional) string $type
Example     : none
Description : Retrives an ArchiveStableId that is the latest incarnation of
              given stable_id. If the lookup fails, attempts to check for a
              version id delimited by a period (.) and lookup again using the
              version id.
Returntype  : Bio::EnsEMBL::ArchiveStableId or undef if not in database
Exceptions  : none
Caller      : general
Status      : At Risk
            : under development

_fetch_by_stable_id

Arg [1]     : string $stable_id
Arg [2]     : (optional) string $type
Example     : none
Description : Retrives an ArchiveStableId that is the latest incarnation of
              given stable_id. Helper function to fetch_by_stable_id, should
              not be directly called.
Returntype  : Bio::EnsEMBL::ArchiveStableId or undef if not in database
Exceptions  : none
Caller      : general
Status      : At Risk
            : under development

fetch_by_stable_id_version

Arg [1]     : string $stable_id
Arg [2]     : int $version
Example     : none
Description : Retrieve an ArchiveStableId with given version and stable ID.
Returntype  : Bio::EnsEMBL::ArchiveStableId 
Exceptions  : none
Caller      : general
Status      : At Risk
            : under development

fetch_by_stable_id_dbname

Arg [1]     : string $stable_id
Arg [2]     : string $db_name
Example     : none
Description : Create an ArchiveStableId from given arguments.
Returntype  : Bio::EnsEMBL::ArchiveStableId or undef if not in database
Exceptions  : none
Caller      : general
Status      : At Risk
            : under development

fetch_all_by_archive_id

Arg [1]     : Bio::EnsEMBL::ArchiveStableId $archive_id
Arg [2]     : String $return_type - type of ArchiveStableId to fetch
Example     : my $arch_id = $arch_adaptor->fetch_by_stable_id('ENSG0001');
              my @archived_transcripts =
               $arch_adaptor->fetch_all_by_archive_id($arch_id, 'Transcript');
Description : Given a ArchiveStableId it retrieves associated ArchiveStableIds
              of specified type (e.g. retrieve transcripts for genes or vice
              versa).

              See also fetch_associated_archived() for a different approach to
              retrieve this data.
Returntype  : listref Bio::EnsEMBL::ArchiveStableId
Exceptions  : none
Caller      : Bio::EnsEMBL::ArchiveStableId->get_all_gene_archive_ids,
              get_all_transcript_archive_ids, get_all_translation_archive_ids
Status      : At Risk
            : under development

fetch_associated_archived

Arg[1]      : Bio::EnsEMBL::ArchiveStableId $arch_id -
              the ArchiveStableId to fetch associated archived IDs for
Example     : my ($arch_gene, $arch_tr, $arch_tl, $pep_seq) =
                @{ $archive_adaptor->fetch_associated_archived($arch_id) };
Description : Fetches associated archived stable IDs from the db for a given
              ArchiveStableId (version is taken into account).
Return type : Listref of
                ArchiveStableId archived gene
                ArchiveStableId archived transcript
                (optional) ArchiveStableId archived translation
                (optional) peptide sequence
Exceptions  : thrown on missing or wrong argument
              thrown if ArchiveStableID has no type
Caller      : Bio::EnsEMBL::ArchiveStableId->get_all_associated_archived()
Status      : At Risk
            : under development

fetch_predecessors_by_archive_id

Arg [1]     : Bio::EnsEMBL::ArchiveStableId
Example     : none
Description : Retrieve a list of ArchiveStableIds that were mapped to the 
              given one. This method goes back only one level, to retrieve
              a full predecessor history use fetch_predecessor_history, or 
              ideally fetch_history_tree_by_stable_id for the complete
              history network.
Returntype  : listref Bio::EnsEMBL::ArchiveStableId
Exceptions  : none
Caller      : Bio::EnsEMBL::ArchiveStableId->get_all_predecessors
Status      : At Risk
            : under development

fetch_successors_by_archive_id

Arg [1]     : Bio::EnsEMBL::ArchiveStableId
Example     : none
Description : Retrieve a list of ArchiveStableIds that the given one was 
              mapped to. This method goes forward only one level, to retrieve
              a full successor history use fetch_successor_history, or 
              ideally fetch_history_tree_by_stable_id for the complete
              history network.
Returntype  : listref Bio::EnsEMBL::ArchiveStableId
Exceptions  : none
Caller      : Bio::EnsEMBL::ArchiveStableId->get_all_successors
Status      : At Risk
            : under development

fetch_history_tree_by_stable_id

Arg [1]     : String $stable_id - the stable ID to fetch the history tree for
Arg [2]     : (optional) Int $num_high_scorers
              number of mappings per stable ID allowed when filtering
Arg [3]     : (optional) Int $max_rows
              maximum number of stable IDs in history tree (used for
              filtering)
Arg [4]     : (optional) Float $time_limit
              Optimise tree normally runs until it hits a minimised state
              but this can take a very long time. Therefore you can
              opt to bail out of the optimisation early. Specify the
              time in seconds. Floating point values are supported should you
              require sub-second limits
Example     : my $history = $archive_adaptor->fetch_history_tree_by_stable_id(
                'ENSG00023747897');
Description : Returns the history tree for a given stable ID. This will
              include a network of all stable IDs it is related to. The
              method will try to return a minimal (sparse) set of nodes
              (ArchiveStableIds) and links (StableIdEvents) by removing any
              redundant entries and consolidating mapping events so that only
              changes are recorded.
Return type : Bio::EnsEMBL::StableIdHistoryTree
Exceptions  : thrown on missing argument
Caller      : Bio::EnsEMBL::ArchiveStableId::get_history_tree, general
Status      : At Risk
            : under development

add_all_current_to_history

Arg[1]      : Bio::EnsEMBL::StableIdHistoryTree $history -
              the StableIdHistoryTree object to add the current IDs to
Description : This method adds the current versions of all stable IDs found
              in a StableIdHistoryTree object to the tree, by creating
              appropriate Events for the stable IDs found in the *_stable_id
              tables. This is a helper method for
              fetch_history_tree_by_stable_id(), see there for more
              documentation.
Return type : none (passed-in object is manipulated)
Exceptions  : thrown on missing or wrong argument
Caller      : internal
Status      : At Risk
            : under development

fetch_successor_history

Arg [1]     : Bio::EnsEMBL::ArchiveStableId $arch_id
Example     : none
Description : Gives back a list of archive stable ids which are successors in
              the stable_id_event tree of the given stable_id. Might well be
              empty.
              
              This method is valid, but in most cases you will rather
              want to use fetch_history_tree_by_stable_id().
Returntype  : listref Bio::EnsEMBL::ArchiveStableId
              Since every ArchiveStableId knows about it's successors, this is
              a linked tree.
Exceptions  : none
Caller      : webcode for archive
Status      : At Risk
            : under development

fetch_predecessor_history

Arg [1]     : Bio::EnsEMBL::ArchiveStableId $arch_id
Example     : none
Description : Gives back a list of archive stable ids which are predecessors
              in the stable_id_event tree of the given stable_id. Might well
              be empty.
              
              This method is valid, but in most cases you will rather
              want to use fetch_history_tree_by_stable_id().
Returntype  : listref Bio::EnsEMBL::ArchiveStableId
              Since every ArchiveStableId knows about it's successors, this is
              a linked tree.
Exceptions  : none
Caller      : webcode for archive
Status      : At Risk
            : under development

fetch_stable_id_event

Arg [1]     : Bio::EnsEMBL::ArchiveStableId $arch_id
Arg [2]     : stable_id
Example     : my $archive = $archive_stable_id_adaptor->fetch_by_stable_id($id);
              my $event = $archive_stable_id_adaptor($archive, $id2);
Description : Gives back the event that links an archive stable id
              to a specific stable id
              
Returntype  : Bio::EnsEMBL::StableIdEvent
              Undef if no event was found
Exceptions  : none
Caller      : general
Status      : At Risk
            : under development

list_dbnames

Args        : none
Example     : none
Description : A list of available database names from the latest (current) to
              the oldest (ordered).
Returntype  : listref of strings
Exceptions  : none
Caller      : general
Status      : At Risk
            : under development

previous_dbname

Arg[1]      : String $dbname - focus db name
Example     : my $prev_db = $self->previous_dbname($curr_db);
Description : Returns the name of the next oldest database which has mapping
              session information.
Return type : String (or undef if not available)
Exceptions  : none
Caller      : general
Status      : At Risk

next_dbname

Arg[1]      : String $dbname - focus db name
Example     : my $prev_db = $self->next_dbname($curr_db);
Description : Returns the name of the next newest database which has mapping
              session information.
Return type : String (or undef if not available)
Exceptions  : none
Caller      : general
Status      : At Risk

get_peptide

Arg [1]     : Bio::EnsEMBL::ArchiveStableId $arch_id
Example     : none
Description : Retrieves the peptide string for given ArchiveStableId. If its
              not a peptide or not in the database returns undef.
Returntype  : string or undef
Exceptions  : none
Caller      : Bio::EnsEMBL::ArchiveStableId->get_peptide, general
Status      : At Risk
            : under development

get_current_release

Example     : my $current_release = $archive_adaptor->get_current_release;
Description : Returns the current release number (as found in the meta table).
Return type : Int
Exceptions  : none
Caller      : general
Status      : At Risk
            : under development

get_current_assembly

Example     : my $current_assembly = $archive_adaptor->get_current_assembly;
Description : Returns the current assembly version (as found in the meta
              table).
Return type : String
Exceptions  : none
Caller      : general
Status      : At Risk
            : under development

lookup_current

Arg[1]      : Bio::EnsEMBL::ArchiveStableId $arch_id -
              the stalbe ID to find the current version for
Example     : if ($self->lookup_version($arch_id) {
                $arch_id->version($arch_id->current_version);
                $arch_id->db_name($self->dbc->dbname);
Description : Look in [gene|transcript|translation]_stable_id if you can find
              a current version for this stable ID. Set
              ArchiveStableId->current_version if found.
Return type : Boolean (TRUE if current version found, else FALSE)
Exceptions  : none
Caller      : general
Status      : At Risk
            : under development