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Bio-EnsEMBL-112.0.0
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/ Bio::EnsEMBL::SeqEdit

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:SeqEdit - A class representing a post transcriptional edit to a sequence.

SYNOPSIS

use Bio::EnsEMBL::SeqEdit;
use Bio::EnsEMBL::Attribute;

# construct a SeqEdit object using a Transcript attribute

($attribute) = @{ $translation->get_all_Attributes('_rna_edit') };

$seq_edit = Bio::EnsEMBL::SeqEdit( -ATTRIB => $attribute );

print $seq_edit->start(),   "\n";
print $seq_edit->end(),     "\n";
print $seq_edit->alt_seq(), "\n";

# apply the edit to some sequence
$seq = $transcript->spliced_seq();
print "Before modifiction: $seq\n";

$seq_edit->apply_edit( \$seq );
print "After modification: $seq\n";

# construct an attribute object from a SeqEdit and add it to a
# translation

$seq_edit = Bio::EnsEMBL::SeqEdit->new(
  -CODE    => '_selenocysteine',
  -NAME    => 'Selenocysteine',
  -DESC    => 'Selenocysteine',
  -START   => 10,
  -END     => 10,
  -ALT_SEQ => 'U'
);

$attribute = $seq_edit->get_Attribute();
$translation->add_Attributes($attribute);

DESCRIPTION

This is a class used to represent post transcriptional modifications to sequences. SeqEdit objects are stored as ordinary Bio::EnsEMBL::Attributes with a parseable value and can be used to represent RNA editing, selenocysteines etc.

Also see Bio::EnsEMBL::Attribute

METHODS

new

Arg [-ATTRIB] : Bio::EnsEMBL::Attribute
                Constructs a new SeqEdit from an Attribute.
                Can only be provided if no other constructor arguments
                are provided.
Arg [-START]       : The start position of the edit.
Arg [-END]         : The end position of the edit.
Arg [-ALT_SEQ]     : The alternate sequence
Arg [-CODE]        : A code for this SeqEdit
Arg [-NAME]        : A name for this SeqEdit
Arg [-DESCRIPTION] : Arg passed to superclass constructor
Example    : my $sea = Bio::EnsEMBL::SeqEdit->new(-ATTRIB => $attrib);
             my $sea = Bio::EnsEMBL::SeqEdit->new
                           (-START => 10,
                            -END   => 12,
                            -ALT_SEQ => 'ACG',
                            -CODE    => '_rna_edit',
                            -NAME    => 'RNA Edit',
                            -DESCRIPTION => 'RNA edit');
Description: Constructs a SeqEdit representing a single edit to a
             sequence, such as an rna modification or a selenocysteine.
Returntype : Bio::EnsEMBL::SeqEdit
Exceptions : throws if attribute set and other args aswell
             throws if start and end not set correctly of attribure not set
Caller     : general
Status     : Stable

start

Arg [1]    : (optional) int $start - the new start position
Example    : $start = $se_attrib->start();
Description: Getter/Setter for the start position of the region replaced
             by the alt_seq.

             Coordinates are inclusive and one-based, which means that
             inserts are unusually represented by a start 1bp higher than
             the end.

             E.g. start = 1, end = 1 is a replacement of the first base but 
             start = 1, end = 0 is an insert BEFORE the first base.
Returntype : int
Exceptions : none
Caller     : Transcript, Translation
Status     : Stable

end

Arg [1]    : (optional) int $end - the new end position
Example    : $end = $se_attrib->end();
Description: Getter/Setter for the end position of the region replaced
             by the alt_seq.

             Coordinates are inclusive and one-based, which means that
             inserts are unusually represented by a start 1bp higher than
             the end.

             E.g. start = 1, end = 1 is a replacement of the first base but
             start = 1, end = 0 is an insert BEFORE the first base.
Returntype : int
Exceptions : throws if end  <= 0
Caller     : Transcript, Translation
Status     : Stable

alt_seq

Arg [1]    : (optional) string $alt_seq
Example    : my $alt_seq = $se_attrib->alt_seq();
Description: Getter/Setter for the replacement sequence used by this edit.
             The sequence may either be a string of amino acids or
             nucleotides depending on the context in which this edit is
             used.

             In the case of a deletion the replacement sequence is an empty
             string.
Returntype : string
Exceptions : none
Caller     : Transcript, Translation
Status     : Stable

length_diff

Arg [1]    : none
Example    : my $diff = $sea->length_diff();
Description: Returns the difference in length caused by applying this
             edit to a sequence.  This may be be negative (deletion),
             positive (insertion) or 0 (replacement).

             If either start or end are not defined 0 is returned.
Returntype : int
Exceptions : none
Caller     : general
Status     : Stable

name

Arg [1]    : (optional) string $name
Example    : my $name = $seqedit->name();
Description: Getter/Setter for the name of this SeqEdit
Returntype : string
Exceptions : none
Caller     : general
Status     : Stable

code

Arg [1]    : (optional) string $code
Example    : my $code = $seqedit->code();
Description: Getter/Setter for the code of this SeqEdit
Returntype : string
Exceptions : none
Caller     : general
Status     : Stable

description

Arg [1]    : (optional) string $desc
Example    : my $desc = $seqedit->description();
Description: Getter/Setter for the description of this SeqEdit
Returntype : string
Exceptions : none
Caller     : general
Status     : Stable

get_Attribute

Arg [1]    : none
Example    : my $attrib = $seqedit->get_Attribute();
             $transcript->add_Attributes($attrib);
Description: Converts a SeqEdit object into an Attribute object.  This
             allows the SeqEdit to be stored as any other attribute in the
             ensembl database.  The start/end and alt_seq properties
             should be set before calling this method.
Returntype : Bio::EnsEMBL::Attribute
Exceptions : warning if start/end or alt_seq properties are not defined
Caller     : general
Status     : Stable

apply_edit

Arg [1]    : reference to string $seqref
Example    : $sequence = 'ACTGAATATTTAAGGCA';
             $seqedit->apply_edit(\$sequence);
             print $sequence, "\n";
Description: Applies this edit directly to a sequence which is
             passed by reference.  The coordinates of this SeqEdit
             are assumed to be relative to the start of the sequence
             argument.
             If either the start or end of this SeqEdit are not defined
             this function will not do anything to the passed sequence.
Returntype : reference to the same sequence that was passed in
Exceptions : none
Caller     : Transcript, Translation
Status     : Stable