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Bio-EnsEMBL-113.0.0
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/ Bio::EnsEMBL::Map::DBSQL::DitagFeatureAdaptor

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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

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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