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Bio-EnsEMBL-113.0.0
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

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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