Sanger::CGP::Vagrent::Data::Transcript - Data object representing a transcript
This is a data class to hold details about a transcript. This allows the transcript information to be abstracted away from its original source.
my $trans = Sanger::CGP::Vagrent::Data::Transcript->new(%params);
Builds a new Sanger::CGP::Vagrent::Data::Transcript object
Sanger::CGP::Vagrent::Data::Transcript object initialized with parameter values
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)
my $name = $trans->getGeneName;
The gene name for the transcript
String
my $type = $trans->getGeneType;
Returns the gene type, will be equal to one of the type constant values
String
my $ccds = $trans->getCCDS;
The CCDS identifier for the transcript
String
my $accession = $trans->getAccession;
The accession of the sequence record for the transcript
String
my $accessionVers = $trans->getAccessionVersion;
The accession verson of the sequence record for the transcript
String
my $protAccession = $trans->getProteinAccession;
The protein accession of the sequence record for the transcript
String
my $protAccessionVers = $trans->getProteinAccessionVersion;
The protein accession verson of the sequence record for the transcript
String
my $sourceDB = $trans->getDatabase;
The name of database the transcript originated from
String
my $sourceDBversion = $trans->getDatabaseVersion;
The version of database the transcript originated from
String
my $genomicMin = $trans->getGenomicMinPos;
The minimum position of the cDNA in the genome
Integer
my $genomicMax = $trans->getGenomicMaxPos;
The maximum position of the cDNA in the genome
Integer
my $strand = $trans->getStrand;
The genomic strand of the transcript
Integer (either 1 or -1)
my $cdsMin = $trans->getCdsMinPos;
The minimum position of the CDS within the cDNA sequence
Integer
my $cdsMax = $trans->getCdsMaxPos;
The maximum position of the CDS within the cDNA sequence
Integer
my $cDNAseq = $trans->getcDNASeq;
The cDNA sequence string
String - DNA sequence
my $phase = $trans->getCdsPhase;
The CDS phase, ie the number of N's needed to append to the start of CDS sequence to create the right translation frame
Integer
my @exons = $trans->getExons;
Returns the Sanger::CGP::Vagrent::Data::Exon objects that make up the transcript sorted into transcript order
Array of Sanger::CGP::Vagrent::Data::Exon objects
my $isCoding = $trans->isProteinCoding; if($trans->isProteinCoding){ ...... }
Convenience function. Returns true if the gene type is protein coding, equivalent to
if($trans->getType eq $trans->getProteinCodingType){ ...... }
Integer boolean (either 1 or 0)
my $CDSseq = $trans->getCdsSeq;
CDS sequence string, ie the subsequence of the cDNA string defined by the CDS min and max coordinates
String - DNA sequence
my $length = $trans->getCdsLength;
The length of the CDS, based on the CDS min and max coordinates on the cDNA
Integer
my $type = $trans->getProteinCodingType(); my $type = Sanger::CGP::Vagrent::Data::Transcript::getProteinCodingType();
Constant lookup, returns the protein coding gene type
String
my $type = $trans->getMicroRnaType(); my $type = Sanger::CGP::Vagrent::Data::Transcript::getMicroRnaType();
Constant lookup, returns the microRNA gene type
String
my $type = $trans->getLincRnaType(); my $type = Sanger::CGP::Vagrent::Data::Transcript::getLincRnaType();
Constant lookup, returns the lincRNA gene type
String
my $type = $trans->getSnoRnaType(); my $type = Sanger::CGP::Vagrent::Data::Transcript::getSnoRnaType();
Constant lookup, returns the snoRNA gene type
String
my $type = $trans->getSnRnaType(); my $type = Sanger::CGP::Vagrent::Data::Transcript::getSnRnaType();
Constant lookup, returns the snRNA gene type
String
my $type = $trans->getRRnaType(); my $type = Sanger::CGP::Vagrent::Data::Transcript::getRRnaType();
Constant lookup, returns the rRNA gene type
String