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Bio-EnsEMBL-113.0.0
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/ Bio::EnsEMBL::Map::DitagFeature

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.

CONTACT

Please email comments or questions to the public Ensembl
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NAME

Bio::EnsEMBL::Map::DitagFeature

SYNOPSIS

my $feature = Bio::EnsEMBL::Map::DitagFeature->new( -slice => $slice, -start => $qstart, -end => $qend, -strand => $qstrand, -hit_start => $tstart, -hit_end => $tend, -hit_strand => $tstrand, -ditag_id => $ditag_id, -ditag_side => $ditag_side, -ditag_pair_id => $ditag_pair_id, -cigar_line => $cigar_line, -analysis => $analysis, );

DESCRIPTION

Represents a mapped ditag object in the EnsEMBL database. These are the original tags separated into start ("L") and end ("R") parts if applicable, successfully aligned to the genome. Two DitagFeatures usually relate to one parent Ditag. Alternatively there are CAGE tags e.g. which only have a 5\'tag ("F").

METHODS

new

Arg [1]    : (optional) int dbID
Arg [2]    : (optional) Bio::EnsEMBL::DitagFeatureAdaptor $adaptor
Arg [3]    : int start
Arg [4]    : int end
Arg [5]    : int strand
Arg [6]    : Bio::EnsEMBL::Slice $slice
Arg [7]    : (optional) Bio::EnsEMBL::Analysis
Arg [8]    : int hit_start
Arg [9]    : int hit_end
Arg [10]   : int hit_strand
Arg [11]   : int ditag_id
Arg [12]   : string ditag_side
Arg [13]   : (optional) sring cigar_line
Arg [14]   : (optional) int ditag_pair_id
Arg [15]   : (optional) int tag_count, only used for imported mappings where
             identical positions where collapsed into into one feature.
             Default: 1
Arg [16]   : (optional) ditag object

Example    : $ditag = Bio::EnsEMBL::Map::DitagFeature->new
                          (-dbID => 123, -adaptor => $adaptor, ...);
Description: Creates a new DitagFeature
Returntype : Bio::EnsEMBL::Map::DitagFeature
Caller     : general
Status     : At Risk

ditag

Arg [1]    : (optional) ditag object
Description: Get/Set the ditag object of this DitagFeature
Returntype : Bio::EnsEMBL::Map::Ditag
Exceptions : none
Caller     : general
Status     : At Risk

get_ditag_location

Arg [1]    : none
Description: Get the start and end location (and strand ) of the start-end pair
             this DitagFeature belongs to.
             If it is not a paired ditag, these will be identical
             to DitagFeature->start() & DitagFeature->end().
             Please note that the returned start/end are min/max locations.
Returntype : int (start, end, strand)
Exceptions : throws if the 2 features of a pair are found on different strands
             or if the second one cannot be found.
Caller     : general
Status     : At Risk

ditag_id

Arg [1]    : (optional) value
Description: Getter/Setter for the ditag_id
             of this DitagFeature
Returntype : int
Exceptions : none
Caller     : general
Status     : At Risk

slice

Arg [1]    : (optional) value
Description: Getter/Setter for the slice
             of this DitagFeature
Returntype : slice object
Exceptions : none
Caller     : general
Status     : At Risk

ditag_pair_id

Arg [1]    : (optional) value
Description: Getter/Setter for the ditag_pair_id
             of this DitagFeature
Returntype : int
Exceptions : none
Caller     : general
Status     : At Risk

ditag_side

Arg [1]    : (optional) value
Description: Getter/Setter for the ditag_side
             of this DitagFeature
Returntype : string
Exceptions : none
Caller     : general
Status     : At Risk

hit_start

Arg [1]    : (optional) value
Description: Getter/Setter for the hit_start
             of this DitagFeature
Returntype : int
Exceptions : none
Caller     : general
Status     : At Risk

hit_end

Arg [1]    : (optional) value
Description: Getter/Setter for the hit_end
             of this DitagFeature
Returntype : int
Exceptions : none
Caller     : general
Status     : At Risk

hit_strand

Arg [1]    : (optional) value
Description: Getter/Setter for the hit_strand
             of this DitagFeature
Returntype : 1/-1/0
Exceptions : none
Caller     : general
Status     : At Risk

cigar_line

Arg [1]    : (optional) value
Description: Getter/Setter for the cigar_line
             of this DitagFeature
Returntype : string
Exceptions : none
Caller     : general
Status     : At Risk

start

Arg [1]    : (optional) value
Description: Getter/Setter for the start
             of this DitagFeature
Returntype : int
Exceptions : none
Caller     : general
Status     : At Risk

end

Arg [1]    : (optional) value
Description: Getter/Setter for the end
             of this DitagFeature
Returntype : int or string
Exceptions : none
Caller     : general
Status     : At Risk

strand

Arg [1]    : (optional) value
Description: Getter/Setter for the strand
             of this DitagFeature
Returntype : 1/-1/0
Exceptions : none
Caller     : general
Status     : At Risk

dbID

Arg [1]    : (optional) value
Description: Getter/Setter for the dbID
             of this DitagFeature
Returntype : int
Exceptions : none
Caller     : general
Status     : At Risk

sequence

Arg [1]    : (optional) value
Description: Getter/Setter for the sequence
             of this DitagFeature
Returntype : string
Exceptions : none
Caller     : general
Status     : At Risk

tag_count

Arg [1]    : (optional) value
Description: Getter/Setter for the tag_count
             of this DitagFeature
Returntype : string
Exceptions : none
Caller     : general
Status     : At Risk