NAME

GenOO::Transcript - Corresponds to a gene transcript

SYNOPSIS

# The class represents a transcript of a gene.
# It extends the L<GenOO::GenomicRegion> class

# Instantiate 
my $transcript = GenOO::Transcript->new(
    name          => undef,
    species       => undef,
    strand        => undef,    #required
    chromosome    => undef,    #required
    start         => undef,    #required
    stop          => undef,    #required
    copy_number   => undef,    #defaults to 1
    sequence      => undef,
    splice_starts => undef,    #required
    splice_stops  => undef,    #required
    id            => undef,    #required
    gene          => undef,    #GenOO::Gene
    utr5          => undef,    #GenOO::Transcript::UTR5
    cds           => undef,    #GenOO::Transcript::CDS
    utr3          => undef,    #GenOO::Transcript::UTR3
    biotype       => undef,
);

DESCRIPTION

The Transcript class describes a transcript of a gene. It can have a backreference
to the gene in which it belongs. Protein coding transcripts have functional regions
such as 5'UTR, CDS and 3'UTR. The transcript class extends the L<GenOO::GenomicRegion>
and implements the L<GenOO::Spliceable> role.

EXAMPLES

# Get the exons of the transcript
$transcript->exons

# Get the introns of the transcript
$transcript->introns

# Check if the transcript codes for a protein
$transcript->is_coding # 0 / 1
$transcript->cds       # undef / GenOO::Transcript::CDS