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package Sanger::CGP::Vagrent::Data::ComplexIndel; |
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##########LICENCE########## |
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# Copyright (c) 2014 Genome Research Ltd. |
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# |
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# Author: Cancer Genome Project cgpit@sanger.ac.uk |
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# |
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# This file is part of VAGrENT. |
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# |
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# VAGrENT is free software: you can redistribute it and/or modify it under |
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# the terms of the GNU Affero General Public License as published by the Free |
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# Software Foundation; either version 3 of the License, or (at your option) any |
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# later version. |
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# |
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# This program is distributed in the hope that it will be useful, but WITHOUT |
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# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS |
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# FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more |
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# details. |
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# |
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# You should have received a copy of the GNU Affero General Public License |
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# along with this program. If not, see <http://www.gnu.org/licenses/>. |
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##########LICENCE########## |
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use strict; |
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use Data::Dumper; |
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use Sanger::CGP::Vagrent qw($VERSION); |
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use base qw(Sanger::CGP::Vagrent::Data::AbstractGenomicPosition Sanger::CGP::Vagrent::Data::AbstractVariation); |
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1; |
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sub _init { |
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my $self = shift; |
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my %vars = @_; |
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foreach my $k(keys(%vars)){ |
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if($k eq 'delseq'){ |
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$self->{_delseq} = $vars{delseq}; |
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} elsif($k eq 'insseq'){ |
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$self->{_insseq} = $vars{insseq}; |
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} |
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} |
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} |
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sub isValid { |
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my $self = shift; |
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return 0 unless(defined($self->{_minpos}) && defined($self->{_maxpos})); |
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return 0 unless($self->{_minpos} <= $self->{_maxpos}); |
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return 0 unless($self->{_minpos} > 0); |
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return 0 unless(defined($self->{_delseq})); |
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return 0 unless(length($self->{_delseq}) > 0); |
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return 0 unless($self->{_delseq} =~ m/^[atcgn]+$/i); |
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return 0 if(length($self->{_delseq}) != ($self->{_maxpos} - $self->{_minpos}) + 1); |
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return 0 unless(exists($self->{_insseq}) && defined($self->{_insseq})); |
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return 0 unless(length($self->{_insseq}) > 0); |
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return 0 unless($self->{_insseq} =~ m/^[atcgn]+$/i); |
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return 1; |
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} |
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sub getDeletedSequence { |
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return shift->{_delseq}; |
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} |
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sub getInsertedSequence { |
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return shift->{_insseq}; |
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} |
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sub toString { |
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my $self = shift; |
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my $out = 'chr'.$self->getChr.':g.'; |
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if($self->getMinPos == $self->getMaxPos){ |
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$out .= $self->getMinPos.'del'.$self->getDeletedSequence; |
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} else { |
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$out .= $self->getMinPos.'_'.$self->getMaxPos.'del'; |
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if(length($self->getDeletedSequence) <= 10){ |
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$out .= $self->getDeletedSequence; |
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} else { |
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$out .= length($self->getDeletedSequence); |
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} |
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} |
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$out .= 'ins'.$self->getInsertedSequence; |
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return $out; |
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} |
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__END__ |
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=head1 NAME |
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Sanger::CGP::Vagrent::Data::ComplexIndel - Data object representing a complex insertion deletion event |
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=head1 DESCRIPTION |
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This is a data class describing a complex insertion/deletion variant plotted to a genome. |
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It inherits from L<Sanger::CGP::Vagrent::Data::AbstractGenomicPosition|Sanger::CGP::Vagrent::Data::AbstractGenomicPosition> and L<Sanger::CGP::Vagrent::Data::AbstractVariation|Sanger::CGP::Vagrent::Data::AbstractVariation> |
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=head1 METHODS |
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=head2 Constructor |
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=head3 new |
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=over |
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=item Usage : |
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my $cplx = Sanger::CGP::Vagrent::Data::ComplexIndel->new(%params); |
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=item Function : |
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Builds a new Sanger::CGP::Vagrent::Data::ComplexIndel object |
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=item Returns : |
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Sanger::CGP::Vagrent::Data::ComplexIndel object initialized with parameter values |
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=item Params : |
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Same as the constructor from L<Sanger::CGP::Vagrent::Data::AbstractGenomicPosition|Sanger::CGP::Vagrent::Data::AbstractGenomicPosition> plus |
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delseq => the deleted sequence fragment |
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insseq => the inserted sequence fragment |
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=back |
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=head2 Attributes |
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=head3 getDeletedSequence |
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=over |
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=item Usage : |
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my $seq = $cplx->getDeletedSequence; |
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=item Function : |
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Returns the deleted sequence fragment |
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=item Returns : |
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String - DNA sequence |
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=back |
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=head3 getInsertedSequence |
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=over |
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=item Usage : |
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my $seq = $cplx->getInsertedSequence; |
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=item Function : |
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Returns the inserted sequence fragment |
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=item Returns : |
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String - DNA sequence |
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=back |
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=head2 Functions |
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=head3 toString |
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=over |
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=item Usage : |
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print $variant->toString; |
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=item Function : |
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Returns a simple string representation of the variant in hgvs genomic syntax |
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=item Returns : |
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String |
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=back |