Class: PositionedGene

Inherits:
Object
  • Object
show all
Defined in:
lib/jgi_genes.rb

Overview

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.

Direct Known Subclasses

PositionedGeneWithOntology

Instance Attribute Summary collapse

Instance Method Summary collapse

Instance Attribute Details

#cds ⇒ Object

Returns the value of attribute cds.



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# File 'lib/jgi_genes.rb', line 137

def cds
  @cds
end

#exons ⇒ Object

Returns the value of attribute exons.



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# File 'lib/jgi_genes.rb', line 137

def exons
  @exons
end

#name ⇒ Object

Returns the value of attribute name.



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# File 'lib/jgi_genes.rb', line 137

def name
  @name
end

#protein_id ⇒ Object

Returns the value of attribute protein_id.



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# File 'lib/jgi_genes.rb', line 137

def protein_id
  @protein_id
end

#seqname ⇒ Object

Returns the value of attribute seqname.



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# File 'lib/jgi_genes.rb', line 137

def seqname
  @seqname
end

#start ⇒ Object

Returns the value of attribute start.



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# File 'lib/jgi_genes.rb', line 137

def start
  @start
end

#strand ⇒ Object

Returns the value of attribute strand.



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# File 'lib/jgi_genes.rb', line 137

def strand
  @strand
end

Instance Method Details

#cds_end ⇒ Object 



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# 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 ⇒ Object

Return the position of the cds end



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# 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? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/jgi_genes.rb', line 156

def positive_strand?
  return @strand === '+'
end