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package Sanger::CGP::Vagrent::TranscriptSource::AbstractTranscriptSource; |
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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 Log::Log4perl; |
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use Carp; |
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use Attribute::Abstract; |
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use Data::Dumper; |
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use Sanger::CGP::Vagrent qw($VERSION); |
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my $log = Log::Log4perl->get_logger(__PACKAGE__); |
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1; |
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sub new { |
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my $proto = shift; |
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my $class = ref($proto) || $proto; |
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my $self = {}; |
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bless($self, $class); |
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$self->_init(@_); |
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return $self; |
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} |
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sub _init: Abstract; |
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sub getTranscripts: Abstract; |
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sub setDumpRegion { |
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my ($self,$gr) = @_; |
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unless(defined($gr) && $gr->isa('Sanger::CGP::Vagrent::Data::AbstractGenomicPosition')){ |
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croak("Did not recieve a Sanger::CGP::Vagrent::Data::AbstractGenomicPosition object"); |
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} |
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$self->{_dumpInfo} = undef; |
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$self->{_dumpInfo}->{_region} = $gr; |
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return; |
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} |
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sub getDumpRegion { |
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my $self = shift; |
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if(defined $self->{_dumpInfo} && defined $self->{_dumpInfo}->{_region}){ |
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return $self->{_dumpInfo}->{_region}; |
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} |
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return undef; |
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} |
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sub isDumpRegionACompleteSequence { |
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my $self = shift; |
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if(defined $self->{_dumpInfo} && defined $self->{_dumpInfo}->{_fullSeq}){ |
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return $self->{_dumpInfo}->{_fullSeq}; |
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} |
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return undef; |
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} |
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sub getTranscriptsForNextGeneInDumpRegion: Abstract; |
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__END__ |
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=head1 NAME |
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Sanger::CGP::Vagrent::TranscriptSource::AbstractTranscriptSource - Abstract base class for Transcript sources |
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=head1 DESCRIPTION |
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This is a base utility class all TranscriptSources should inherit from, its little more than an interface with the vast majority of the functionality being implemented in the sub class. |
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Sub classes must implement a getTranscripts method and an internal _init method. |
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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 $source = Sanger::CGP::Vagrent::TranscriptSource::AbstractTranscriptSourceSubClass->new(); |
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=item Function : |
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Builds a new Sanger::CGP::Vagrent::TranscriptSource::AbstractTranscriptSource inheriting object |
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=item Returns : |
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Sanger::CGP::Vagrent::TranscriptSource::AbstractTranscriptSource object initialized with parameter values |
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=item Params : |
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Hash of parameter values, the actual keys/values required depend on the sub class. |
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=back |
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=head2 Attributes |
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=head3 setDumpRegion |
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=over |
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=item Usage : |
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$source->setDumpRegion($genomicPosition); |
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=item Function : |
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Sets the L<GenomicRegion|Sanger::CGP::Vagrent::Data::AbstractGenomicPosition> to seed Transcript/Gene set retrieval |
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=item Returns : |
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Nothing |
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=item Params : |
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Any L<Sanger::CGP::Vagrent::Data::AbstractGenomicPosition|Sanger::CGP::Vagrent::Data::AbstractGenomicPosition> implementing object |
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=back |
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=head3 getDumpRegion |
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=over |
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=item Usage : |
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my $region = $source->getDumpRegion(); |
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=item Function : |
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Gets the L<GenomicRegion|Sanger::CGP::Vagrent::Data::AbstractGenomicPosition> used to seed Transcript/Gene set retrieval |
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=item Returns : |
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A L<Sanger::CGP::Vagrent::Data::AbstractGenomicPosition|Sanger::CGP::Vagrent::Data::AbstractGenomicPosition> implementing object or undef |
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=back |
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=head2 Functions |
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=head3 isDumpRegionACompleteSequence |
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=over |
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=item Usage : |
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if($source->isDumpRegionACompleteSequence()){ |
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...... |
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} |
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=item Function : |
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Returns boolean status for the current dump region being a complete sequence (eg. a whole chromosome/contig). The value behind this is populated by getTranscriptsForNextGeneInDumpRegion method when processing the specified gene region |
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=item Returns : |
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A Boolean, 1 if it is a complete sequence, 0 if is isn't or undef if it doesn't know |
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=back |
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=head2 Abstract |
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=head3 getTranscripts |
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=over |
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=item Usage : |
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my @transList = $source->getTranscripts($genomicPosition); |
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=item Function : |
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Abstract function, must be overridden by a subclass. Retrieves a list of L<Transcripts|Sanger::CGP::Vagrent::Data::Transcript> objects overlapping the specified L<GenomicPosition|Sanger::CGP::Vagrent::Data::AbstractGenomicPosition> |
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=item Returns : |
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An array of L<Sanger::CGP::Vagrent::Data::Transcript|Sanger::CGP::Vagrent::Data::Transcript> objects |
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=item Params : |
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Any L<Sanger::CGP::Vagrent::Data::AbstractGenomicPosition|Sanger::CGP::Vagrent::Data::AbstractGenomicPosition> implementing object |
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=back |
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=head3 getTranscriptsForNextGeneInDumpRegion |
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=over |
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=item Usage : |
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while (my @transList = $source->getTranscriptsForNextGeneInDumpRegion()){ |
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.... |
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} |
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=item Function : |
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Abstract function, must be overridden by a subclass. Retrieves a list of L<Transcripts|Sanger::CGP::Vagrent::Data::Transcript> objects belonging to the next gene inside the previously specified L<GenomicRegion|Sanger::CGP::Vagrent::Data::AbstractGenomicPosition> |
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=item Returns : |
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An array of L<Sanger::CGP::Vagrent::Data::Transcript|Sanger::CGP::Vagrent::Data::Transcript> objects |
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=item Params : |
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None |
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=back |
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=head3 _init |
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=over |
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=item Usage : |
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$self->_init(@params); |
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=item Function : |
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Abstract internal function, must be overridden by a subclass. This method is used to handle constructor parameters, its called by new. |
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=item Returns : |
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None |
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=item Params : |
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The flattened array of key/value pairs passed in from new. |
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=back |