class PositionedGene

A gene as read from the gff file. cds and exons are assumed to be in increasing order in terms of their positions along the positive strand.

Attributes

cds[RW]
exons[RW]
name[RW]
protein_id[RW]
seqname[RW]
start[RW]
strand[RW]

Public Instance Methods

cds_end() click to toggle source
# File lib/jgi_genes.rb, line 148
def cds_end
  # If gene has no coding regions, I guess
  if !@cds[@cds.length-1]
    return nil
  end
  return @cds[@cds.length-1].to
end
cds_start() click to toggle source

Return the position of the cds end

# File lib/jgi_genes.rb, line 140
def cds_start
  # If gene has no coding regions, I guess
  if !@cds[0]
    return nil
  end
  return @cds[0].from
end
positive_strand?() click to toggle source
# File lib/jgi_genes.rb, line 156
def positive_strand?
  return @strand === '+'
end