class Bio::Sequence::NA

Attributes

mut_pos[RW]

Public Instance Methods

dist_from_polvs() click to toggle source

return an array of distances from each polv

# File lib/bio/sequence/na/na.rb, line 53
def dist_from_polvs
  [polv1_dna_pos, polv2_dna_pos, polv3_dna_pos, polv4_dna_pos]
end

polv1_dna_pos() click to toggle source

# File lib/bio/sequence/na/na.rb, line 36
def polv1_dna_pos
  mut_pos.map{|mut| mut - (aa_seq.polv1_pos * 3)}
end

polv2_dna_pos() click to toggle source

# File lib/bio/sequence/na/na.rb, line 40
def polv2_dna_pos
  mut_pos.map{|mut| mut - (aa_seq.polv2_pos * 3)}
end

polv3_dna_pos() click to toggle source

# File lib/bio/sequence/na/na.rb, line 44
def polv3_dna_pos
  mut_pos.map{|mut| mut - (aa_seq.polv3_pos * 3)}
end

polv4_dna_pos() click to toggle source

# File lib/bio/sequence/na/na.rb, line 48
def polv4_dna_pos
  mut_pos.map{|mut| mut - (aa_seq.polv4_pos * 3)}
end

pspb1_dna(anchor_pos=0,win_len=42) click to toggle source

position specific polymorphic block 1

# File lib/bio/sequence/na/na.rb, line 5
def pspb1_dna(anchor_pos=0,win_len=42)
  self[42 + anchor_pos,win_len]
end

pspb2_dna(anchor_pos=0,win_len=42) click to toggle source

position specific polymorphic block 2

# File lib/bio/sequence/na/na.rb, line 10
def pspb2_dna(anchor_pos=0,win_len=42)
  if !ww_missing?
    return self[(ww_pos * 3) - 12 - anchor_pos - win_len, win_len]
  elsif !vw_missing?
    return self[(vw_pos * 3) - 36 - win_len - anchor_pos, win_len]
  else
    return '....'
  end
end

pspb3_dna(anchor_pos=0,win_len=42) click to toggle source

position specific polymorphic block 3

# File lib/bio/sequence/na/na.rb, line 21
def pspb3_dna(anchor_pos=0,win_len=42)
  if !ww_missing?
    return self[(ww_pos * 3) + 42 + anchor_pos, win_len]
  elsif !vw_missing?
    return self[(vw_pos * 3) + 8 + anchor_pos, win_len]
  else
    return '....'
  end
end

pspb4_dna(anchor_pos=0,win_len=42) click to toggle source

position specific polymorphic block 4

# File lib/bio/sequence/na/na.rb, line 32
def pspb4_dna(anchor_pos=0,win_len=42)
  self[self.length - 36 - win_len - anchor_pos, win_len]
end

Private Instance Methods

aa_seq() click to toggle source

# File lib/bio/sequence/na/na.rb, line 62
def aa_seq
  self.translate
end

accepted_length() click to toggle source

# File lib/bio/sequence/na/na.rb, line 58
def accepted_length
  aa_seq.accepted_length #300..500
end

vw_missing?() click to toggle source

# File lib/bio/sequence/na/na.rb, line 78
def vw_missing?
  aa_seq.vw_missing? #true unless aa_seq =~ /VW/i
end

vw_pos() click to toggle source

# File lib/bio/sequence/na/na.rb, line 70
def vw_pos
  aa_seq.vw_pos #rindex("VW")
end

vw_ww_missing?() click to toggle source

# File lib/bio/sequence/na/na.rb, line 82
def vw_ww_missing?
  aa_seq.vw_ww_missing? #true if ww_missing? && vw_missing?
end

ww_missing?() click to toggle source

# File lib/bio/sequence/na/na.rb, line 74
def ww_missing?
  aa_seq.ww_missing? #true unless aa_seq =~ /WW/i
end

ww_pos() click to toggle source

# File lib/bio/sequence/na/na.rb, line 66
def ww_pos
  aa_seq.ww_pos #rindex("WW")
end