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package Sanger::CGP::Vagrent::Data::Transcript; |
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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 Carp; |
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use Data::Dumper; |
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use Sanger::CGP::Vagrent qw($VERSION); |
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use Sort::Key qw(nkeysort); |
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use Const::Fast qw(const); |
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use base qw(Sanger::CGP::Vagrent); |
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const my $PROTEIN_CODING_TYPE => 'ProteinCoding'; |
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const my $MIRCO_RNA_TYPE => 'miRNA'; |
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const my $LINC_RNA_TYPE => 'lincRNA'; |
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const my $SNO_RNA_TYPE => 'snoRNA'; |
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const my $SN_RNA_TYPE => 'snRNA'; |
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const my $R_RNA_TYPE => 'rRNA'; |
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const my @ALL_GENE_TYPES => ($PROTEIN_CODING_TYPE,$MIRCO_RNA_TYPE,$LINC_RNA_TYPE,$SNO_RNA_TYPE,$SN_RNA_TYPE,$R_RNA_TYPE); |
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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 { |
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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 'db'){ |
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$self->{_db} = $vars{db}; |
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} elsif($k eq 'dbversion'){ |
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$self->{_dbversion} = $vars{dbversion}; |
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} elsif($k eq 'exons' && ref($vars{exons}) eq 'ARRAY'){ |
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$self->{_exons} = $vars{exons}; |
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} elsif($k eq 'strand'){ |
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$self->{_strand} = $vars{strand}; |
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} elsif($k eq 'genomicminpos'){ |
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$self->{_genomicminpos} = $vars{genomicminpos}; |
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} elsif($k eq 'genomicmaxpos'){ |
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$self->{_genomicmaxpos} = $vars{genomicmaxpos}; |
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} elsif($k eq 'cdnaseq'){ |
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$self->{_cdnaseq} = $vars{cdnaseq}; |
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} elsif($k eq 'cdsphase'){ |
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$self->{_cdsphase} = $vars{cdsphase}; |
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} elsif($k eq 'cdsminpos'){ |
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$self->{_cdsminpos} = $vars{cdsminpos}; |
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} elsif($k eq 'cdsmaxpos'){ |
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$self->{_cdsmaxpos} = $vars{cdsmaxpos}; |
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} elsif($k eq 'acc'){ |
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$self->{_acc} = $vars{acc}; |
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} elsif($k eq 'accversion'){ |
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$self->{_accversion} = $vars{accversion}; |
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} elsif($k eq 'proteinacc'){ |
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$self->{_proteinacc} = $vars{proteinacc}; |
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} elsif($k eq 'proteinaccversion'){ |
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$self->{_proteinaccversion} = $vars{proteinaccversion}; |
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} elsif($k eq 'ccds'){ |
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$self->{_ccds} = $vars{ccds}; |
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} elsif($k eq 'genename'){ |
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$self->{_genename} = $vars{genename}; |
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} elsif($k eq 'genetype'){ |
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$self->{_genetype} = $vars{genetype}; |
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my $good = undef; |
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foreach my $type(@ALL_GENE_TYPES){ |
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if($vars{genetype} eq $type){ |
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$good = $vars{genetype}; |
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last; |
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} |
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} |
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if(defined($good)){ |
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$self->{_genetype} = $good; |
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} else { |
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croak('recieved unknown gene type: '.$vars{genetype}); |
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} |
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} |
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} |
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} |
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sub getAllGeneTypes { |
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return @ALL_GENE_TYPES; |
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} |
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sub getGeneType { |
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return shift->{_genetype}; |
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} |
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sub getCCDS { |
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return shift->{_ccds}; |
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} |
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sub getGeneName { |
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return shift->{_genename}; |
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} |
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sub getAccession { |
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return shift->{_acc}; |
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} |
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sub getAccessionVersion { |
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return shift->{_accversion}; |
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} |
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sub getProteinAccession { |
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return shift->{_proteinacc}; |
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} |
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sub getProteinAccessionVersion { |
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return shift->{_proteinaccversion}; |
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} |
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sub getDatabase { |
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return shift->{_db}; |
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} |
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sub getDatabaseVersion { |
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return shift->{_dbversion}; |
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} |
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sub getExons { |
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my $self = shift; |
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return nkeysort {$_->getRnaMinPos} @{$self->{_exons}}; |
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} |
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sub getExonsGenomicOrder { |
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my $self = shift; |
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return nkeysort {$_->getMinPos} @{$self->{_exons}}; |
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} |
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sub getStrand { |
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return shift->{_strand}; |
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} |
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sub getcDNASeq { |
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return shift->{_cdnaseq}; |
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} |
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sub getCdsSeq { |
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my $self = shift; |
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return substr($self->{_cdnaseq},($self->{_cdsminpos} - 1),(($self->{_cdsmaxpos} - $self->{_cdsminpos}) + 1)); |
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} |
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sub getCdsPhase { |
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return shift->{_cdsphase}; |
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} |
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sub getCdsMinPos { |
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return shift->{_cdsminpos}; |
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} |
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sub getCdsMaxPos { |
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return shift->{_cdsmaxpos}; |
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} |
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sub getCdsLength { |
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my $self = shift; |
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unless(defined($self->{_cdslength})){ |
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$self->{_cdslength} = ($self->getCdsMaxPos - $self->getCdsMinPos) + 1; |
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} |
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return $self->{_cdslength}; |
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} |
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sub getmRNALength { |
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my $self = shift; |
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unless(defined $self->{_mrnalength}){ |
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my $size = 0; |
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foreach my $e (@{$self->{_exons}}){ |
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$size += $e->getLength(); |
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} |
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$self->{_mrnalength} = $size; |
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} |
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return $self->{_mrnalength}; |
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} |
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sub getGenomicMinPos { |
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return shift->{_genomicminpos}; |
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} |
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sub getGenomicMaxPos { |
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return shift->{_genomicmaxpos}; |
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} |
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sub isProteinCoding { |
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if(shift->getGeneType eq $PROTEIN_CODING_TYPE){ |
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return 1; |
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} else { |
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return 0; |
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} |
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} |
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sub getProteinCodingType { |
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return $PROTEIN_CODING_TYPE; |
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} |
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sub getMicroRnaType { |
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return $MIRCO_RNA_TYPE; |
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} |
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sub getLincRnaType { |
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return $LINC_RNA_TYPE; |
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} |
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sub getSnoRnaType { |
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return $SNO_RNA_TYPE; |
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} |
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sub getSnRnaType { |
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return $SN_RNA_TYPE; |
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} |
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sub getRRnaType { |
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return $R_RNA_TYPE; |
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} |
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__END__ |
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=head1 NAME |
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Sanger::CGP::Vagrent::Data::Transcript - Data object representing a transcript |
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=head1 DESCRIPTION |
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This is a data class to hold details about a transcript. This allows the transcript information |
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to be abstracted away from its original source. |
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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 $trans = Sanger::CGP::Vagrent::Data::Transcript->new(%params); |
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=item Function : |
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Builds a new Sanger::CGP::Vagrent::Data::Transcript object |
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=item Returns : |
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Sanger::CGP::Vagrent::Data::Transcript object initialized with parameter values |
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=item Params : |
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db => source DB the transcript came from |
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dbversion => version of the source DB |
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exons => array ref of Sanger::CGP::Vagrent::Data::Exon objects |
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strand => Genomic strand of the transcript (1 or -1) |
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cdnaseq => cDNA sequence string |
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cdsminpos => CDS minimum coordinate in the cDNA sequence |
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cdsmaxpos => CDS maximum coordinate in the cDNA sequence |
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cdsphase => The phase of translation on the CDS (ie the number of N's to add to the begining of the CDS to make it translate) |
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acc => Transcript accession number (typically the cDNA accession) |
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accversion => Version of the transcript accession number |
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proteinacc => Protein accession number (optional) |
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proteinaccversion => Version of the protein accession number (optional) |
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ccds => CCDS id for the transcript (optional) |
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genename => Gene name |
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genetype => Gene type (defined by type constant) |
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=back |
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=head2 Attributes |
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=head3 getGeneName |
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=over |
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=item Usage : |
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my $name = $trans->getGeneName; |
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=item Function |
307
|
|
|
|
|
308
|
|
|
|
The gene name for the transcript |
309
|
|
|
|
|
310
|
|
|
|
=item Returns |
311
|
|
|
|
|
312
|
|
|
|
String |
313
|
|
|
|
|
314
|
|
|
|
=back |
315
|
|
|
|
|
316
|
|
|
|
=head3 getGeneType |
317
|
|
|
|
|
318
|
|
|
|
=over |
319
|
|
|
|
|
320
|
|
|
|
=item Usage : |
321
|
|
|
|
|
322
|
|
|
|
my $type = $trans->getGeneType; |
323
|
|
|
|
|
324
|
|
|
|
=item Function |
325
|
|
|
|
|
326
|
|
|
|
Returns the gene type, will be equal to one of the type constant values |
327
|
|
|
|
|
328
|
|
|
|
=item Returns |
329
|
|
|
|
|
330
|
|
|
|
String |
331
|
|
|
|
|
332
|
|
|
|
=back |
333
|
|
|
|
|
334
|
|
|
|
=head3 getCCDS |
335
|
|
|
|
|
336
|
|
|
|
=over |
337
|
|
|
|
|
338
|
|
|
|
=item Usage : |
339
|
|
|
|
|
340
|
|
|
|
my $ccds = $trans->getCCDS; |
341
|
|
|
|
|
342
|
|
|
|
=item Function |
343
|
|
|
|
|
344
|
|
|
|
The CCDS identifier for the transcript |
345
|
|
|
|
|
346
|
|
|
|
=item Returns |
347
|
|
|
|
|
348
|
|
|
|
String |
349
|
|
|
|
|
350
|
|
|
|
=back |
351
|
|
|
|
|
352
|
|
|
|
=head3 getAccession |
353
|
|
|
|
|
354
|
|
|
|
=over |
355
|
|
|
|
|
356
|
|
|
|
=item Usage : |
357
|
|
|
|
|
358
|
|
|
|
my $accession = $trans->getAccession; |
359
|
|
|
|
|
360
|
|
|
|
=item Function |
361
|
|
|
|
|
362
|
|
|
|
The accession of the sequence record for the transcript |
363
|
|
|
|
|
364
|
|
|
|
=item Returns |
365
|
|
|
|
|
366
|
|
|
|
String |
367
|
|
|
|
|
368
|
|
|
|
=back |
369
|
|
|
|
|
370
|
|
|
|
=head3 getAccessionVersion |
371
|
|
|
|
|
372
|
|
|
|
=over |
373
|
|
|
|
|
374
|
|
|
|
=item Usage : |
375
|
|
|
|
|
376
|
|
|
|
my $accessionVers = $trans->getAccessionVersion; |
377
|
|
|
|
|
378
|
|
|
|
=item Function |
379
|
|
|
|
|
380
|
|
|
|
The accession verson of the sequence record for the transcript |
381
|
|
|
|
|
382
|
|
|
|
=item Returns |
383
|
|
|
|
|
384
|
|
|
|
String |
385
|
|
|
|
|
386
|
|
|
|
=back |
387
|
|
|
|
|
388
|
|
|
|
=head3 getProteinAccession |
389
|
|
|
|
|
390
|
|
|
|
=over |
391
|
|
|
|
|
392
|
|
|
|
=item Usage : |
393
|
|
|
|
|
394
|
|
|
|
my $protAccession = $trans->getProteinAccession; |
395
|
|
|
|
|
396
|
|
|
|
=item Function |
397
|
|
|
|
|
398
|
|
|
|
The protein accession of the sequence record for the transcript |
399
|
|
|
|
|
400
|
|
|
|
=item Returns |
401
|
|
|
|
|
402
|
|
|
|
String |
403
|
|
|
|
|
404
|
|
|
|
=back |
405
|
|
|
|
|
406
|
|
|
|
=head3 getProteinAccessionVersion |
407
|
|
|
|
|
408
|
|
|
|
=over |
409
|
|
|
|
|
410
|
|
|
|
=item Usage : |
411
|
|
|
|
|
412
|
|
|
|
my $protAccessionVers = $trans->getProteinAccessionVersion; |
413
|
|
|
|
|
414
|
|
|
|
=item Function |
415
|
|
|
|
|
416
|
|
|
|
The protein accession verson of the sequence record for the transcript |
417
|
|
|
|
|
418
|
|
|
|
=item Returns |
419
|
|
|
|
|
420
|
|
|
|
String |
421
|
|
|
|
|
422
|
|
|
|
=back |
423
|
|
|
|
|
424
|
|
|
|
=head3 getDatabase |
425
|
|
|
|
|
426
|
|
|
|
=over |
427
|
|
|
|
|
428
|
|
|
|
=item Usage : |
429
|
|
|
|
|
430
|
|
|
|
my $sourceDB = $trans->getDatabase; |
431
|
|
|
|
|
432
|
|
|
|
=item Function |
433
|
|
|
|
|
434
|
|
|
|
The name of database the transcript originated from |
435
|
|
|
|
|
436
|
|
|
|
=item Returns |
437
|
|
|
|
|
438
|
|
|
|
String |
439
|
|
|
|
|
440
|
|
|
|
=back |
441
|
|
|
|
|
442
|
|
|
|
=head3 getDatabaseVersion |
443
|
|
|
|
|
444
|
|
|
|
=over |
445
|
|
|
|
|
446
|
|
|
|
=item Usage : |
447
|
|
|
|
|
448
|
|
|
|
my $sourceDBversion = $trans->getDatabaseVersion; |
449
|
|
|
|
|
450
|
|
|
|
=item Function |
451
|
|
|
|
|
452
|
|
|
|
The version of database the transcript originated from |
453
|
|
|
|
|
454
|
|
|
|
=item Returns |
455
|
|
|
|
|
456
|
|
|
|
String |
457
|
|
|
|
|
458
|
|
|
|
=back |
459
|
|
|
|
|
460
|
|
|
|
=head3 getGenomicMinPos |
461
|
|
|
|
|
462
|
|
|
|
=over |
463
|
|
|
|
|
464
|
|
|
|
=item Usage : |
465
|
|
|
|
|
466
|
|
|
|
my $genomicMin = $trans->getGenomicMinPos; |
467
|
|
|
|
|
468
|
|
|
|
=item Function |
469
|
|
|
|
|
470
|
|
|
|
The minimum position of the cDNA in the genome |
471
|
|
|
|
|
472
|
|
|
|
=item Returns |
473
|
|
|
|
|
474
|
|
|
|
Integer |
475
|
|
|
|
|
476
|
|
|
|
=back |
477
|
|
|
|
|
478
|
|
|
|
=head3 getGenomicMaxPos |
479
|
|
|
|
|
480
|
|
|
|
=over |
481
|
|
|
|
|
482
|
|
|
|
=item Usage : |
483
|
|
|
|
|
484
|
|
|
|
my $genomicMax = $trans->getGenomicMaxPos; |
485
|
|
|
|
|
486
|
|
|
|
=item Function |
487
|
|
|
|
|
488
|
|
|
|
The maximum position of the cDNA in the genome |
489
|
|
|
|
|
490
|
|
|
|
=item Returns |
491
|
|
|
|
|
492
|
|
|
|
Integer |
493
|
|
|
|
|
494
|
|
|
|
=back |
495
|
|
|
|
|
496
|
|
|
|
=head3 getStrand |
497
|
|
|
|
|
498
|
|
|
|
=over |
499
|
|
|
|
|
500
|
|
|
|
=item Usage : |
501
|
|
|
|
|
502
|
|
|
|
my $strand = $trans->getStrand; |
503
|
|
|
|
|
504
|
|
|
|
=item Function |
505
|
|
|
|
|
506
|
|
|
|
The genomic strand of the transcript |
507
|
|
|
|
|
508
|
|
|
|
=item Returns |
509
|
|
|
|
|
510
|
|
|
|
Integer (either 1 or -1) |
511
|
|
|
|
|
512
|
|
|
|
=back |
513
|
|
|
|
|
514
|
|
|
|
=head3 getCdsMinPos |
515
|
|
|
|
|
516
|
|
|
|
=over |
517
|
|
|
|
|
518
|
|
|
|
=item Usage : |
519
|
|
|
|
|
520
|
|
|
|
my $cdsMin = $trans->getCdsMinPos; |
521
|
|
|
|
|
522
|
|
|
|
=item Function |
523
|
|
|
|
|
524
|
|
|
|
The minimum position of the CDS within the cDNA sequence |
525
|
|
|
|
|
526
|
|
|
|
=item Returns |
527
|
|
|
|
|
528
|
|
|
|
Integer |
529
|
|
|
|
|
530
|
|
|
|
=back |
531
|
|
|
|
|
532
|
|
|
|
=head3 getCdsMaxPos |
533
|
|
|
|
|
534
|
|
|
|
=over |
535
|
|
|
|
|
536
|
|
|
|
=item Usage : |
537
|
|
|
|
|
538
|
|
|
|
my $cdsMax = $trans->getCdsMaxPos; |
539
|
|
|
|
|
540
|
|
|
|
=item Function |
541
|
|
|
|
|
542
|
|
|
|
The maximum position of the CDS within the cDNA sequence |
543
|
|
|
|
|
544
|
|
|
|
=item Returns |
545
|
|
|
|
|
546
|
|
|
|
Integer |
547
|
|
|
|
|
548
|
|
|
|
=back |
549
|
|
|
|
|
550
|
|
|
|
=head3 getcDNASeq |
551
|
|
|
|
|
552
|
|
|
|
=over |
553
|
|
|
|
|
554
|
|
|
|
=item Usage : |
555
|
|
|
|
|
556
|
|
|
|
my $cDNAseq = $trans->getcDNASeq; |
557
|
|
|
|
|
558
|
|
|
|
=item Function |
559
|
|
|
|
|
560
|
|
|
|
The cDNA sequence string |
561
|
|
|
|
|
562
|
|
|
|
=item Returns |
563
|
|
|
|
|
564
|
|
|
|
String - DNA sequence |
565
|
|
|
|
|
566
|
|
|
|
=back |
567
|
|
|
|
|
568
|
|
|
|
=head3 getCdsPhase |
569
|
|
|
|
|
570
|
|
|
|
=over |
571
|
|
|
|
|
572
|
|
|
|
=item Usage : |
573
|
|
|
|
|
574
|
|
|
|
my $phase = $trans->getCdsPhase; |
575
|
|
|
|
|
576
|
|
|
|
=item Function |
577
|
|
|
|
|
578
|
|
|
|
The CDS phase, ie the number of N's needed to append to the start of CDS sequence to create the right translation frame |
579
|
|
|
|
|
580
|
|
|
|
=item Returns |
581
|
|
|
|
|
582
|
|
|
|
Integer |
583
|
|
|
|
|
584
|
|
|
|
=back |
585
|
|
|
|
|
586
|
|
|
|
=head3 getExons |
587
|
|
|
|
|
588
|
|
|
|
=over |
589
|
|
|
|
|
590
|
|
|
|
=item Usage : |
591
|
|
|
|
|
592
|
|
|
|
my @exons = $trans->getExons; |
593
|
|
|
|
|
594
|
|
|
|
=item Function |
595
|
|
|
|
|
596
|
|
|
|
Returns the Sanger::CGP::Vagrent::Data::Exon objects that make up the transcript sorted into transcript order |
597
|
|
|
|
|
598
|
|
|
|
=item Returns |
599
|
|
|
|
|
600
|
|
|
|
Array of Sanger::CGP::Vagrent::Data::Exon objects |
601
|
|
|
|
|
602
|
|
|
|
=back |
603
|
|
|
|
|
604
|
|
|
|
=head2 Functions |
605
|
|
|
|
|
606
|
|
|
|
=head3 isProteinCoding |
607
|
|
|
|
|
608
|
|
|
|
=over |
609
|
|
|
|
|
610
|
|
|
|
=item Usage : |
611
|
|
|
|
|
612
|
|
|
|
my $isCoding = $trans->isProteinCoding; |
613
|
|
|
|
|
614
|
|
|
|
if($trans->isProteinCoding){ |
615
|
|
|
|
...... |
616
|
|
|
|
} |
617
|
|
|
|
|
618
|
|
|
|
=item Function |
619
|
|
|
|
|
620
|
|
|
|
Convenience function. Returns true if the gene type is protein coding, equivalent to |
621
|
|
|
|
|
622
|
|
|
|
if($trans->getType eq $trans->getProteinCodingType){ |
623
|
|
|
|
...... |
624
|
|
|
|
} |
625
|
|
|
|
|
626
|
|
|
|
|
627
|
|
|
|
=item Returns |
628
|
|
|
|
|
629
|
|
|
|
Integer boolean (either 1 or 0) |
630
|
|
|
|
|
631
|
|
|
|
=back |
632
|
|
|
|
|
633
|
|
|
|
=head3 getCdsSeq |
634
|
|
|
|
|
635
|
|
|
|
=over |
636
|
|
|
|
|
637
|
|
|
|
=item Usage : |
638
|
|
|
|
|
639
|
|
|
|
my $CDSseq = $trans->getCdsSeq; |
640
|
|
|
|
|
641
|
|
|
|
=item Function |
642
|
|
|
|
|
643
|
|
|
|
CDS sequence string, ie the subsequence of the cDNA string defined by the CDS min and max coordinates |
644
|
|
|
|
|
645
|
|
|
|
=item Returns |
646
|
|
|
|
|
647
|
|
|
|
String - DNA sequence |
648
|
|
|
|
|
649
|
|
|
|
=back |
650
|
|
|
|
|
651
|
|
|
|
=head3 getCdsLength |
652
|
|
|
|
|
653
|
|
|
|
=over |
654
|
|
|
|
|
655
|
|
|
|
=item Usage : |
656
|
|
|
|
|
657
|
|
|
|
my $length = $trans->getCdsLength; |
658
|
|
|
|
|
659
|
|
|
|
=item Function |
660
|
|
|
|
|
661
|
|
|
|
The length of the CDS, based on the CDS min and max coordinates on the cDNA |
662
|
|
|
|
|
663
|
|
|
|
=item Returns |
664
|
|
|
|
|
665
|
|
|
|
Integer |
666
|
|
|
|
|
667
|
|
|
|
=back |
668
|
|
|
|
|
669
|
|
|
|
=head2 Constants |
670
|
|
|
|
|
671
|
|
|
|
=head3 getProteinCodingType |
672
|
|
|
|
|
673
|
|
|
|
=over |
674
|
|
|
|
|
675
|
|
|
|
=item Usage : |
676
|
|
|
|
|
677
|
|
|
|
my $type = $trans->getProteinCodingType(); |
678
|
|
|
|
my $type = Sanger::CGP::Vagrent::Data::Transcript::getProteinCodingType(); |
679
|
|
|
|
|
680
|
|
|
|
=item Function : |
681
|
|
|
|
|
682
|
|
|
|
Constant lookup, returns the protein coding gene type |
683
|
|
|
|
|
684
|
|
|
|
=item Returns : |
685
|
|
|
|
|
686
|
|
|
|
String |
687
|
|
|
|
|
688
|
|
|
|
=back |
689
|
|
|
|
|
690
|
|
|
|
=head3 getMicroRnaType |
691
|
|
|
|
|
692
|
|
|
|
=over |
693
|
|
|
|
|
694
|
|
|
|
=item Usage : |
695
|
|
|
|
|
696
|
|
|
|
my $type = $trans->getMicroRnaType(); |
697
|
|
|
|
my $type = Sanger::CGP::Vagrent::Data::Transcript::getMicroRnaType(); |
698
|
|
|
|
|
699
|
|
|
|
=item Function : |
700
|
|
|
|
|
701
|
|
|
|
Constant lookup, returns the microRNA gene type |
702
|
|
|
|
|
703
|
|
|
|
=item Returns : |
704
|
|
|
|
|
705
|
|
|
|
String |
706
|
|
|
|
|
707
|
|
|
|
=back |
708
|
|
|
|
|
709
|
|
|
|
=head3 getLincRnaType |
710
|
|
|
|
|
711
|
|
|
|
=over |
712
|
|
|
|
|
713
|
|
|
|
=item Usage : |
714
|
|
|
|
|
715
|
|
|
|
my $type = $trans->getLincRnaType(); |
716
|
|
|
|
my $type = Sanger::CGP::Vagrent::Data::Transcript::getLincRnaType(); |
717
|
|
|
|
|
718
|
|
|
|
=item Function : |
719
|
|
|
|
|
720
|
|
|
|
Constant lookup, returns the lincRNA gene type |
721
|
|
|
|
|
722
|
|
|
|
=item Returns : |
723
|
|
|
|
|
724
|
|
|
|
String |
725
|
|
|
|
|
726
|
|
|
|
=back |
727
|
|
|
|
|
728
|
|
|
|
=head3 getSnoRnaType |
729
|
|
|
|
|
730
|
|
|
|
=over |
731
|
|
|
|
|
732
|
|
|
|
=item Usage : |
733
|
|
|
|
|
734
|
|
|
|
my $type = $trans->getSnoRnaType(); |
735
|
|
|
|
my $type = Sanger::CGP::Vagrent::Data::Transcript::getSnoRnaType(); |
736
|
|
|
|
|
737
|
|
|
|
=item Function : |
738
|
|
|
|
|
739
|
|
|
|
Constant lookup, returns the snoRNA gene type |
740
|
|
|
|
|
741
|
|
|
|
=item Returns : |
742
|
|
|
|
|
743
|
|
|
|
String |
744
|
|
|
|
|
745
|
|
|
|
=back |
746
|
|
|
|
|
747
|
|
|
|
=head3 getSnRnaType |
748
|
|
|
|
|
749
|
|
|
|
=over |
750
|
|
|
|
|
751
|
|
|
|
=item Usage : |
752
|
|
|
|
|
753
|
|
|
|
my $type = $trans->getSnRnaType(); |
754
|
|
|
|
my $type = Sanger::CGP::Vagrent::Data::Transcript::getSnRnaType(); |
755
|
|
|
|
|
756
|
|
|
|
=item Function : |
757
|
|
|
|
|
758
|
|
|
|
Constant lookup, returns the snRNA gene type |
759
|
|
|
|
|
760
|
|
|
|
=item Returns : |
761
|
|
|
|
|
762
|
|
|
|
String |
763
|
|
|
|
|
764
|
|
|
|
=back |
765
|
|
|
|
|
766
|
|
|
|
=head3 getRRnaType |
767
|
|
|
|
|
768
|
|
|
|
=over |
769
|
|
|
|
|
770
|
|
|
|
=item Usage : |
771
|
|
|
|
|
772
|
|
|
|
my $type = $trans->getRRnaType(); |
773
|
|
|
|
my $type = Sanger::CGP::Vagrent::Data::Transcript::getRRnaType(); |
774
|
|
|
|
|
775
|
|
|
|
=item Function : |
776
|
|
|
|
|
777
|
|
|
|
Constant lookup, returns the rRNA gene type |
778
|
|
|
|
|
779
|
|
|
|
=item Returns : |
780
|
|
|
|
|
781
|
|
|
|
String |
782
|
|
|
|
|
783
|
|
|
|
=back |