Raw content of Bio::EnsEMBL::SeqEdit
<![CDATA[=head1 LICENSE
Copyright (c) 1999-2009 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license.
For license details, please see
/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=cut
=head1 NAME
Bio::EnsEMBL:SeqEdit - A class representing a post transcriptional edit to a
sequence.
=head1 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);
=head1 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 B<Bio::EnsEMBL::Attribute>
=head1 METHODS
=cut
package Bio::EnsEMBL::SeqEdit;
use strict;
use warnings;
use Bio::EnsEMBL::Attribute;
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Bio::EnsEMBL::Utils::Exception qw(throw);
=head2 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
=cut
sub new {
my $class = shift;
my ($attrib, $start, $end, $alt_seq, $name, $desc, $code) =
rearrange([qw(ATTRIB START END ALT_SEQ NAME DESCRIPTION CODE)], @_);
my $self;
if($attrib) {
if(defined($start) || defined($end) || defined($alt_seq) ||
defined($name) || defined($desc) || defined($code)) {
throw("Cannot specify -ATTRIB argument with additional arguments.");
}
if(!ref($attrib) || !$attrib->isa('Bio::EnsEMBL::Attribute')) {
throw('Bio::EnsEMBL::Attribute argument expected.');
}
($start, $end, $alt_seq) = split(/\s+/, $attrib->value());
if($start !~ /\d+/ || $end !~ /\d+/) {
throw('Could not parse value of attribute: '.$attrib->value());
}
$name = $attrib->name();
$code = $attrib->code();
$desc = $attrib->description();
}
if(defined($end) && defined($start) && $start > $end+1) {
throw("start must be less than or equal to end + 1");
}
if(defined($start) && $start < 1) {
throw("start must be greater than or equal to 1");
}
if(defined($end) && $end < 0) {
throw("end must be greater than or equal to 0");
}
$alt_seq ||= '';
return bless {'start' => $start,
'end' => $end,
'alt_seq' => $alt_seq,
'description' => $desc,
'name' => $name,
'code' => $code}, $class;
}
=head2 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
=cut
sub start {
my $self = shift;
if(@_) {
my $start = shift;
if(defined($start) && $start < 1) {
throw("start must be greater than or equal to 1");
}
$self->{'start'} = $start;
}
return $self->{'start'};
}
=head2 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
=cut
sub end {
my $self = shift;
if(@_) {
my $end = shift;
if(defined($end) && $end < 0) {
throw("end must be greater than or equal to 0");
}
$self->{'end'} = $end;
}
return $self->{'end'};
}
=head2 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
=cut
sub alt_seq {
my $self = shift;
$self->{'alt_seq'} = shift || '' if(@_);
return $self->{'alt_seq'};
}
=head2 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
=cut
sub length_diff {
my $self = shift;
return 0 if(!defined($self->{'end'}) || !defined($self->{'start'}));
return length($self->{'alt_seq'}) - ($self->{'end'} - $self->{'start'} + 1);
}
=head2 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
=cut
sub name {
my $self = shift;
$self->{'name'} = shift if(@_);
return $self->{'name'};
}
=head2 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
=cut
sub code {
my $self = shift;
$self->{'code'} = shift if(@_);
return $self->{'code'};
}
=head2 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
=cut
sub description {
my $self = shift;
$self->{'description'} = shift if(@_);
return $self->{'description'};
}
=head2 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
=cut
sub get_Attribute {
my $self = shift;
my $start = $self->start();
my $end = $self->end();
my $alt_seq = $self->alt_seq();
my $value;
if(defined($start) && defined($end) && defined($alt_seq)) {
$value = join(' ', $start, $end, $alt_seq);
} else {
warning('Attribute value cannot be created unless start, end and alt_seq' .
'properties are defined');
$value = '';
}
return Bio::EnsEMBL::Attribute->new(-CODE => $self->code(),
-VALUE => $value,
-NAME => $self->name(),
-DESCRIPTION => $self->description());
}
=head2 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
=cut
sub apply_edit {
my $self = shift;
my $seqref = shift;
if(ref($seqref) ne 'SCALAR') {
throw("Reference to scalar argument expected");
}
if(!defined($self->{'start'}) || !defined($self->{'end'})) {
return $seqref;
}
my $len = $self->{'end'} - $self->{'start'} + 1;
substr($$seqref, $self->{'start'} - 1, $len) = $self->{'alt_seq'};
return $seqref;
}
1;
]]>