[BioRuby] locus mixin

[Jan Aerts]

What do people think about adding a IsLocus mixin to bioruby? For a lot of
my work I need to check if genes or polymorphisms or clones or ... overlap.
I use the IsLocus mixin to get that done. Any object that has a chromosome,
start and stop can have the module mixed in. Some of the methods as I have
them defined locally:
module IsLocus
  def range
    return Range.new(self.start, self.stop)
  end

  def overlaps?(other_locus)
    return false if self.chromosome != other_locus.chromosome

    if self.range.overlaps?(other_locus.range)
      return true
    end

    return false
  end

  def contained_by?(other_locus)
    return false if self.chromosome != other_locus.chromosome

    if self.range.contained_by?(other_locus.range)
      return true
    end

    return false
  end

  def contains?(other_locus)
    return false if self.chromosome != other_locus.chromosome

    if self.range.contains?(other_locus.range)
      return true
    end

    return false
  end

  def to_s
    return self.chromosome + ':' + self.range.to_s
  end

  def to_gff3
    return [self.chromosome, self.class.name, self.start, self.stop, '.',
'.', '.', 'ID=' + self.id.to_s].join("\t")
  end

  def to_bed
    if self.respond_to?(:name)
      return [self.chromosome, self.start, self.stop, self.name].join("\t")
    else
      return [self.chromosome, self.start, self.stop, self.class.name + '_'
+ self.id.to_s].join("\t")
    end
  end

  # The following makes it possible to call Gene#to_bed which would dump all
Gene objects in BED format
  def self.included mod
    class << mod
      def to_bed
        output = Array.new
        output.push("track name='#{self.name}' description='#{self.name}'")
        self.all.each do |record|
          output.push record.to_bed
        end
        return output.join("\n")
      end
    end
  end
end

Let me know what you think,
jan.