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package Sanger::CGP::Vagrent::Data::Exon; |
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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); |
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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 'rnaminpos'){ |
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$self->{_rnaminpos} = $vars{rnaminpos}; |
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} elsif($k eq 'rnamaxpos'){ |
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$self->{_rnamaxpos} = $vars{rnamaxpos}; |
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} |
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} |
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} |
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sub getRnaMinPos { |
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return shift->{_rnaminpos}; |
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} |
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sub getRnaMaxPos { |
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return shift->{_rnamaxpos}; |
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} |
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sub toString { |
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my $self = shift; |
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print $self->getChr.':'.$self->getMinPos.'..'.$self->getMaxPos; |
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} |
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__END__ |
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=head1 NAME |
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Sanger::CGP::Vagrent::Data::Exon - Data object representing an exon |
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=head1 DESCRIPTION |
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This is a data class to hold details about an exon. This allows the exon information to be |
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abstracted away from its original source. |
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It inherits from L<Sanger::CGP::Vagrent::Data::AbstractGenomicPosition|Sanger::CGP::Vagrent::Data::AbstractGenomicPosition> |
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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 $exon = Sanger::CGP::Vagrent::Data::Exon->new(%params); |
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=item Function : |
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Builds a new Sanger::CGP::Vagrent::Data::Exon object |
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=item Returns : |
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Sanger::CGP::Vagrent::Data::Exon 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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rnaminpos => minimum position of the exon in the mRNA |
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rnamaxpos => maximum position of the exon in the mRNA |
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=back |
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=head2 Attributes |
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=head3 getRnaMinPos |
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=over |
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=item Usage : |
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my $rnaMin = $exon->getRnaMinPos; |
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=item Function : |
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Returns the exons minimum position in the rna sequence |
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=item Returns : |
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Integer |
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=back |
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=head3 getRnaMaxPos |
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=over |
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=item Usage : |
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my $rnaMax = $exon->getRnaMaxPos; |
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=item Function : |
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Returns the exons maximum position in the rna sequence |
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=item Returns : |
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Integer |
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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 $exon->toString; |
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=item Function : |
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Returns a simple string representation of the genomic view of the exon (chr:min..max) |
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=item Returns : |
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String |
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=back |