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::Map::DBSQL::DitagFeatureAdaptor

SYNOPSIS

  my $dfa = $db->get_DitagFeatureAdaptor;
  my $ditagFeatures = $dfa->fetch_all_by_Slice( $slice, "SME005" );

  foreach my $ditagFeature (@$ditagFeatures) {
    print $ditagFeature->ditag_id . " "
      . $ditagFeature->slice . " "
      . $ditagFeature->start . "-"
      . $ditagFeature->end . " "
      . $ditagFeature->strand;
  }

DESCRIPTION

Provides database interaction for the Bio::EnsEMBL::Map::DitagFeature object

METHODS

fetch_all

  Arg [1]    : none
  Example    : @all_tags = @{$ditagfeature_adaptor->fetch_all};
  Description: Retrieves all ditagFeatures from the database;
               Usually not a good idea, use fetch_all_by_Slice instead.
  Returntype : listref of Bio::EnsEMBL::Map::DitagFeature
  Caller     : general
  Status     : At Risk

fetch_by_dbID

  Arg [1]    : ditagFeature dbID
  Example    : @my_tags = @{$ditagfeature_adaptor->fetch_by_dbID($my_id)};
  Description: Retrieves a ditagFeature from the database.
  Returntype : Bio::EnsEMBL::Map::DitagFeature
  Caller     : general
  Status     : At Risk

fetch_all_by_ditagID

  Arg [1]    : ditag dbID
  Arg [2]    : (optional) ditag-pair dbID
  Arg [3]    : (optional) analysis ID
  Example    : @my_tags = @{$ditagfeature_adaptor->fetch_all_by_ditag_id($my_id)};
  Description: Retrieves all ditagFeatures from the database linking to a specific ditag-id
  Returntype : listref of Bio::EnsEMBL::Map::DitagFeature
  Caller     : general
  Status     : At Risk

fetch_all_by_type

  Arg [1]    : ditag type
  Example    : @my_tags = @{$ditagfeature_adaptor->fetch_all_by_type($type)};
  Description: Retrieves all ditagFeatures from the database linking to a specific ditag-type
  Returntype : listref of Bio::EnsEMBL::Map::DitagFeature
  Caller     : general
  Status     : At Risk

fetch_all_by_Slice

  Arg [1]    : Bio::EnsEMBL::Slice
  Arg [2]    : (optional) ditag type name (specific library) or an aray ref with multiple type names
  Arg [3]    : (optional) analysis logic_name
  Example    : $tags = $ditagfeature_adaptor->fetch_all_by_Slice($slice, "SME005");
  Description: Retrieves ditagFeatures from the database overlapping a specific region
               and (optional) of a specific ditag type or analysis.
               Start & end locations are returned in slice coordinates, now.
  Returntype : listref of Bio::EnsEMBL::Map::DitagFeatures
  Caller     : general
  Status     : At Risk

fetch_pairs_by_Slice

  Arg [1]    : Bio::EnsEMBL::Slice
  Arg [2]    : (optional) ditag type (specific library)
  Arg [3]    : (optional) analysis logic_name
  Example    : my $ditagfeatures = $dfa->fetch_pairs_by_Slice($slice);
               foreach my $ditagfeature (@$ditagfeatures){
                 $minstart   = $$ditagfeature2{'start'};
                 $maxend     = $$ditagfeature2{'end'};
                 $bothstrand = $$ditagfeature2{'strand'};
                 $tag_count  = $$ditagfeature2{'tag_count'};
                 print "$minstart, $maxend, $bothstrand, $tag_count\n";
               }
  Description: Retrieves ditagFeature information in pairs from the database overlapping a specific region
               and (optional) of a specific ditag type or analysis. The absotute start and end points are
               fetched.
               Slices should be SMALL!
  Returntype : array ref with hash ref of artifical DitagFeature object
  Caller     : general
  Status     : At Risk

_fetch

  Arg [1]    : statement handler
  Arg [2]    : (optional) target-slice for the feature
  Description: generic sql-fetch function for the DitagFeature fetch methods
  Returntype : listref of Bio::EnsEMBL::Map::DitagFeatures
  Caller     : private
  Status     : At Risk

sequence

  Arg [1]    : dbID of DitagFeature
  Example    : $ditagfeature_adaptor->get_sequence($ditagFeature->dbID)
  Description: get the part of the sequence of a ditag,
               that is actully aligned to the genome.
  Returntype : string
  Exceptions : thrown if not all data needed for storing is populated in the
               ditag features
  Caller     : Bio::EnsEMBL::Map::DitagFeature
  Status     : At Risk

store

  Arg [1]    : (Array ref of) Bio::EnsEMBL::Map::DitagFeature
  Example    : $ditagfeature_adaptor->store(@ditag_features);
  Description: Stores a single ditagFeature or
               a list of ditagFeatures in this database.
  Returntype : none
  Exceptions : thrown if not all data needed for storing is populated in the
               ditag features
  Caller     : general
  Status     : At Risk

batch_store

  Arg [1]    : (Array ref of) Bio::EnsEMBL::Map::DitagFeatures
  Arg [2]    : bool have_dbIDs
  Example    : $ditagfeature_adaptor->batch_store(\@ditag_features);
  Description: Stores a list of ditagFeatures in this database.
               DitagFeatures are expected to have no dbID yet unless flag "have_dbIDs" is true.
               They are inserted in one combined INSERT for better performance.
  Returntype : none
  Exceptions : thrown if not all data needed for storing is given for the
               ditag features
  Caller     : general
  Status     : At Risk

update

  Arg [1]    : ditagFeature to update
  Description: update an existing ditagFeature with new values
  Returntype : 1 on success
  Status     : At Risk

list_dbIDs

  Args       : None
  Example    : my @feature_ids = @{$dfa->list_dbIDs()};
  Description: Gets an array of internal IDs for all DitagFeature objects in
               the current database.
  Arg[1]     : <optional> int. not 0 for the ids to be sorted by the seq_region.
  Returntype : List of ints
  Exceptions : None
  Status     : Stable

cpanm Bio::EnsEMBL

perl -MCPAN -e shell
install Bio::EnsEMBL