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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CONTACT

  Please email comments or questions to the public Ensembl
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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

cpanm Bio::EnsEMBL

perl -MCPAN -e shell
install Bio::EnsEMBL