/ 
GenOO-1.5.2
River stage one • 3 direct dependents • 3 total dependents
/ GenOO::Gene

NAME

GenOO::Gene - Gene object

SYNOPSIS

# This object represents a gene (collection of transcripts)
# It extends the L<GenOO::GenomicRegion> object

# To initialize 
my $gene = GenOO::Gene->new(
    name        => undef,    #required
    species     => undef,
    strand      => undef,    #can be inferred from transcripts
    chromosome  => undef,    #can be inferred from transcripts
    start       => undef,    #can be inferred from transcripts
    stop        => undef,    #can be inferred from transcripts
    copy_number => undef,    #defaults to 1
    sequence    => undef,
    description => undef,
    transcripts => reference to an array of L<GenOO::Transcript> objects
);

DESCRIPTION

GenOO::Gene describes a gene. A gene is defined as a genomic region (it has the strand, chromosome, start and stop
attributes required by L<GenOO::GenomicRegion>) as well as collection of L<GenOO::Transcript> objects. The genomic
location attributes can be inferred by the locations of the contained transcripts. The start position of the gene
will be the smallest coordinate of all the contained transcripts etc.
Whenever a transcript is added to a gene object the genomic coordinates of the gene are automatically updated.
It is a good idea NOT to set the genomic location of the gene directly but to let it be inferred by the transcripts.

EXAMPLES # Create a new gene object my $gene = GenOO::Gene->new( name => '2310016C08Rik', description => 'hypoxia-inducible gene 2 protein isoform 2', transcripts => [ GenOO::Transcript->new( id => 'uc012eiw.1', strand => 1, chromosome => 'chr6', start => 29222487, stop => 29225448, coding_start => 29222571, coding_stop => 29224899, biotype => 'coding', splice_starts => [29222487,29224649], splice_stops => [29222607,29225448] ), GenOO::Transcript->new( id => 'uc009bdd.2', strand => 1, chromosome => 'chr6', start => 29222625, stop => 29225448, coding_start => 29224705, coding_stop => 29224899, biotype => 'coding', splice_starts => [29222625,29224649], splice_stops => [29222809,29225448] ) ], );

# Get gene information
$gene->strand;     # 1
$gene->chromosome; # chr6
$gene->start;      # 29222487
$gene->stop;       # 29225448