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NAME

Sanger::CGP::Vagrent::Data::Transcript - Data object representing a transcript

DESCRIPTION

This is a data class to hold details about a transcript. This allows the transcript information to be abstracted away from its original source.

METHODS

Constructor

new

Usage :
 my $trans = Sanger::CGP::Vagrent::Data::Transcript->new(%params);
Function :

Builds a new Sanger::CGP::Vagrent::Data::Transcript object

Returns :

Sanger::CGP::Vagrent::Data::Transcript object initialized with parameter values

Params :
 db                => source DB the transcript came from
 dbversion         => version of the source DB
 exons             => array ref of Sanger::CGP::Vagrent::Data::Exon objects
 strand            => Genomic strand of the transcript (1 or -1)
 cdnaseq           => cDNA sequence string
 cdsminpos         => CDS minimum coordinate in the cDNA sequence
 cdsmaxpos         => CDS maximum coordinate in the cDNA sequence
 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)
 acc               => Transcript accession number (typically the cDNA accession)
 accversion        => Version of the transcript accession number
 proteinacc        => Protein accession number (optional)
 proteinaccversion => Version of the protein accession number (optional)
 ccds              => CCDS id for the transcript (optional)
 genename          => Gene name
 genetype          => Gene type (defined by type constant)

Attributes

getGeneName

Usage :
 my $name = $trans->getGeneName;
Function

The gene name for the transcript

Returns

String

getGeneType

Usage :
 my $type = $trans->getGeneType;
Function

Returns the gene type, will be equal to one of the type constant values

Returns

String

getCCDS

Usage :
 my $ccds = $trans->getCCDS;
Function

The CCDS identifier for the transcript

Returns

String

getAccession

Usage :
 my $accession = $trans->getAccession;
Function

The accession of the sequence record for the transcript

Returns

String

getAccessionVersion

Usage :
 my $accessionVers = $trans->getAccessionVersion;
Function

The accession verson of the sequence record for the transcript

Returns

String

getProteinAccession

Usage :
 my $protAccession = $trans->getProteinAccession;
Function

The protein accession of the sequence record for the transcript

Returns

String

getProteinAccessionVersion

Usage :
 my $protAccessionVers = $trans->getProteinAccessionVersion;
Function

The protein accession verson of the sequence record for the transcript

Returns

String

getDatabase

Usage :
 my $sourceDB = $trans->getDatabase;
Function

The name of database the transcript originated from

Returns

String

getDatabaseVersion

Usage :
 my $sourceDBversion = $trans->getDatabaseVersion;
Function

The version of database the transcript originated from

Returns

String

getGenomicMinPos

Usage :
 my $genomicMin = $trans->getGenomicMinPos;
Function

The minimum position of the cDNA in the genome

Returns

Integer

getGenomicMaxPos

Usage :
 my $genomicMax = $trans->getGenomicMaxPos;
Function

The maximum position of the cDNA in the genome

Returns

Integer

getStrand

Usage :
 my $strand = $trans->getStrand;
Function

The genomic strand of the transcript

Returns

Integer (either 1 or -1)

getCdsMinPos

Usage :
 my $cdsMin = $trans->getCdsMinPos;
Function

The minimum position of the CDS within the cDNA sequence

Returns

Integer

getCdsMaxPos

Usage :
 my $cdsMax = $trans->getCdsMaxPos;
Function

The maximum position of the CDS within the cDNA sequence

Returns

Integer

getcDNASeq

Usage :
 my $cDNAseq = $trans->getcDNASeq;
Function

The cDNA sequence string

Returns

String - DNA sequence

getCdsPhase

Usage :
 my $phase = $trans->getCdsPhase;
Function

The CDS phase, ie the number of N's needed to append to the start of CDS sequence to create the right translation frame

Returns

Integer

getExons

Usage :
 my @exons = $trans->getExons;
Function

Returns the Sanger::CGP::Vagrent::Data::Exon objects that make up the transcript sorted into transcript order

Returns

Array of Sanger::CGP::Vagrent::Data::Exon objects

Functions

isProteinCoding

Usage :
 my $isCoding = $trans->isProteinCoding;

 if($trans->isProteinCoding){
   ......
 }
Function

Convenience function. Returns true if the gene type is protein coding, equivalent to

 if($trans->getType eq $trans->getProteinCodingType){
   ......
 }
Returns

Integer boolean (either 1 or 0)

getCdsSeq

Usage :
 my $CDSseq = $trans->getCdsSeq;
Function

CDS sequence string, ie the subsequence of the cDNA string defined by the CDS min and max coordinates

Returns

String - DNA sequence

getCdsLength

Usage :
 my $length = $trans->getCdsLength;
Function

The length of the CDS, based on the CDS min and max coordinates on the cDNA

Returns

Integer

Constants

getProteinCodingType

Usage :
 my $type = $trans->getProteinCodingType();
 my $type = Sanger::CGP::Vagrent::Data::Transcript::getProteinCodingType();
Function :

Constant lookup, returns the protein coding gene type

Returns :

String

getMicroRnaType

Usage :
 my $type = $trans->getMicroRnaType();
 my $type = Sanger::CGP::Vagrent::Data::Transcript::getMicroRnaType();
Function :

Constant lookup, returns the microRNA gene type

Returns :

String

getLincRnaType

Usage :
 my $type = $trans->getLincRnaType();
 my $type = Sanger::CGP::Vagrent::Data::Transcript::getLincRnaType();
Function :

Constant lookup, returns the lincRNA gene type

Returns :

String

getSnoRnaType

Usage :
 my $type = $trans->getSnoRnaType();
 my $type = Sanger::CGP::Vagrent::Data::Transcript::getSnoRnaType();
Function :

Constant lookup, returns the snoRNA gene type

Returns :

String

getSnRnaType

Usage :
 my $type = $trans->getSnRnaType();
 my $type = Sanger::CGP::Vagrent::Data::Transcript::getSnRnaType();
Function :

Constant lookup, returns the snRNA gene type

Returns :

String

getRRnaType

Usage :
 my $type = $trans->getRRnaType();
 my $type = Sanger::CGP::Vagrent::Data::Transcript::getRRnaType();
Function :

Constant lookup, returns the rRNA gene type

Returns :

String

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