Class: Bio::Sequence::NA

Inherits:
String show all
Includes:
Common
Defined in:
lib/bio/sequence/na.rb,
lib/bio/sequence/compat.rb,
lib/bio/shell/plugin/midi.rb

Overview

– TODO

- add "Ohno" style
- add a accessor to drum pattern
- add a new feature to select music style (pop, trans, ryukyu, ...)
- what is the base?

++

Direct Known Subclasses

RestrictionEnzyme::SingleStrand

Defined Under Namespace

Classes: MidiTrack

Class Method Summary collapse

Instance Method Summary collapse

Methods included from Common

#+, #<<, #composition, #concat, #normalize!, #randomize, #seq, #splice, #subseq, #to_fasta, #to_s, #total, #window_search

Methods inherited from String

#fill, #fold, #skip, #step, #to_aaseq, #to_naseq

Constructor Details

#initialize(str) ⇒ NA

Generate an nucleic acid sequence object from a string.

s = Bio::Sequence::NA.new("aagcttggaccgttgaagt")

or maybe (if you have an nucleic acid sequence in a file)

s = Bio::Sequence:NA.new(File.open('dna.txt').read)

Nucleic Acid sequences are always all lowercase in bioruby

s = Bio::Sequence::NA.new("AAGcTtGG")
puts s                                  #=> "aagcttgg"

Whitespace is stripped from the sequence

seq = Bio::Sequence::NA.new("atg\nggg\ttt\r  gc")
puts s                                  #=> "atggggttgc"

Arguments:

  • (required) str: String

Returns

Bio::Sequence::NA object



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# File 'lib/bio/sequence/na.rb', line 75

def initialize(str)
  super
  self.downcase!
  self.tr!(" \t\n\r",'')
end

Class Method Details

.randomize(*arg, &block) ⇒ Object

Generate a new random sequence with the given frequency of bases. The sequence length is determined by their cumulative sum. (See also Bio::Sequence::Common#randomize which creates a new randomized sequence object using the base composition of an existing sequence instance).

counts = {'a'=>1,'c'=>2,'g'=>3,'t'=>4}
puts Bio::Sequence::NA.randomize(counts)  #=> "ggcttgttac" (for example)

You may also feed the output of randomize into a block

actual_counts = {'a'=>0, 'c'=>0, 'g'=>0, 't'=>0}
Bio::Sequence::NA.randomize(counts) {|x| actual_counts[x] += 1}
actual_counts                     #=> {"a"=>1, "c"=>2, "g"=>3, "t"=>4}

Arguments:

  • (optional) hash: Hash object

Returns

Bio::Sequence::NA object



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# File 'lib/bio/sequence/compat.rb', line 82

def self.randomize(*arg, &block)
  self.new('').randomize(*arg, &block)
end

Instance Method Details

#at_content ⇒ Object

Calculate the ratio of AT / ATGC bases. U is regarded as T.

s = Bio::Sequence::NA.new('atggcgtga')
puts s.at_content                       #=> 0.444444444444444
Returns

Float



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# File 'lib/bio/sequence/na.rb', line 317

def at_content
  count = self.composition
  at = count['a'] + count['t'] + count['u']
  gc = count['g'] + count['c']
  return 0.0 if at + gc == 0
  return at.quo(at + gc)
end

#at_skew ⇒ Object

Calculate the ratio of (A - T) / (A + T) bases. U is regarded as T.

s = Bio::Sequence::NA.new('atgttgttgttc')
puts s.at_skew                          #=> -0.75
Returns

Float



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# File 'lib/bio/sequence/na.rb', line 345

def at_skew
  count = self.composition
  a = count['a']
  t = count['t'] + count['u']
  return 0.0 if a + t == 0
  return (a - t).quo(a + t)
end

#codon_usage ⇒ Object

Returns counts of each codon in the sequence in a hash.

s = Bio::Sequence::NA.new('atggcgtga')
puts s.codon_usage                #=> {"gcg"=>1, "tga"=>1, "atg"=>1}

This method does not validate codons! Any three letter group is a ‘codon’. So,

s = Bio::Sequence::NA.new('atggNNtga')
puts s.codon_usage                #=> {"tga"=>1, "gnn"=>1, "atg"=>1}

seq = Bio::Sequence::NA.new('atgg--tga')
puts s.codon_usage                #=> {"tga"=>1, "g--"=>1, "atg"=>1}

Also, there is no option to work in any frame other than the first.

Returns

Hash object



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# File 'lib/bio/sequence/na.rb', line 273

def codon_usage
  hash = Hash.new(0)
  self.window_search(3, 3) do |codon|
    hash[codon] += 1
  end
  return hash
end

#cut_with_enzyme(*args) ⇒ Object Also known as: cut_with_enzymes

Example:

seq = Bio::Sequence::NA.new('gaattc')
cuts = seq.cut_with_enzyme('EcoRI')

or

seq = Bio::Sequence::NA.new('gaattc')
cuts = seq.cut_with_enzyme('g^aattc')

See Bio::RestrictionEnzyme::Analysis.cut



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# File 'lib/bio/sequence/na.rb', line 479

def cut_with_enzyme(*args)
  Bio::RestrictionEnzyme::Analysis.cut(self, *args)
end

#dna ⇒ Object

Returns a new sequence object with any ‘u’ bases changed to ‘t’. The original sequence is not modified.

s = Bio::Sequence::NA.new('augc')
puts s.dna                              #=> 'atgc'
puts s                                  #=> 'augc'
Returns

new Bio::Sequence::NA object



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# File 'lib/bio/sequence/na.rb', line 423

def dna
  self.tr('u', 't')
end

#dna! ⇒ Object

Changes any ‘u’ bases in the original sequence to ‘t’. The original sequence is modified.

s = Bio::Sequence::NA.new('augc')
puts s.dna!                             #=> 'atgc'
puts s                                  #=> 'atgc'
Returns

current Bio::Sequence::NA object (modified)



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# File 'lib/bio/sequence/na.rb', line 435

def dna!
  self.tr!('u', 't')
end

#forward_complement ⇒ Object

Returns a new complementary sequence object (without reversing). The original sequence object is not modified.

s = Bio::Sequence::NA.new('atgc')
puts s.forward_complement               #=> 'tacg'
puts s                                  #=> 'atgc'
Returns

new Bio::Sequence::NA object



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# File 'lib/bio/sequence/na.rb', line 100

def forward_complement
  s = self.class.new(self)
  s.forward_complement!
  s
end

#forward_complement! ⇒ Object

Converts the current sequence into its complement (without reversing). The original sequence object is modified.

seq = Bio::Sequence::NA.new('atgc')
puts s.forward_complement!              #=> 'tacg'
puts s                                  #=> 'tacg'
Returns

current Bio::Sequence::NA object (modified)



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# File 'lib/bio/sequence/na.rb', line 114

def forward_complement!
  if self.rna?
    self.tr!('augcrymkdhvbswn', 'uacgyrkmhdbvswn')
  else
    self.tr!('atgcrymkdhvbswn', 'tacgyrkmhdbvswn')
  end
  self
end

#gc_content ⇒ Object

Calculate the ratio of GC / ATGC bases. U is regarded as T.

s = Bio::Sequence::NA.new('atggcgtga')
puts s.gc_content                       #=> 0.555555555555556
Returns

Float



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# File 'lib/bio/sequence/na.rb', line 303

def gc_content
  count = self.composition
  at = count['a'] + count['t'] + count['u']
  gc = count['g'] + count['c']
  return 0.0 if at + gc == 0
  return gc.quo(at + gc)
end

#gc_percent ⇒ Object

Calculate the ratio of GC / ATGC bases as a percentage rounded to the nearest whole number. U is regarded as T.

s = Bio::Sequence::NA.new('atggcgtga')
puts s.gc_percent                       #=> 55
Returns

Fixnum



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# File 'lib/bio/sequence/na.rb', line 288

def gc_percent
  count = self.composition
  at = count['a'] + count['t'] + count['u']
  gc = count['g'] + count['c']
  return 0 if at + gc == 0
  gc = 100 * gc / (at + gc)
  return gc
end

#gc_skew ⇒ Object

Calculate the ratio of (G - C) / (G + C) bases.

s = Bio::Sequence::NA.new('atggcgtga')
puts s.gc_skew                          #=> 0.6
Returns

Float



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# File 'lib/bio/sequence/na.rb', line 331

def gc_skew
  count = self.composition
  g = count['g']
  c = count['c']
  return 0.0 if g + c == 0
  return (g - c).quo(g + c)
end

#illegal_bases ⇒ Object

Returns an alphabetically sorted array of any non-standard bases (other than ‘atgcu’).

s = Bio::Sequence::NA.new('atgStgQccR')
puts s.illegal_bases                    #=> ["q", "r", "s"]
Returns

Array object



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# File 'lib/bio/sequence/na.rb', line 360

def illegal_bases
  self.scan(/[^atgcu]/).sort.uniq
end

#molecular_weight ⇒ Object

Estimate molecular weight (using the values from BioPerl’s SeqStats.pm module).

s = Bio::Sequence::NA.new('atggcgtga')
puts s.molecular_weight                 #=> 2841.00708

RNA and DNA do not have the same molecular weights,

s = Bio::Sequence::NA.new('auggcguga')
puts s.molecular_weight                 #=> 2956.94708
Returns

Float object



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# File 'lib/bio/sequence/na.rb', line 376

def molecular_weight
  if self.rna?
    Bio::NucleicAcid.weight(self, true)
  else
    Bio::NucleicAcid.weight(self)
  end
end

#names ⇒ Object

Generate the list of the names of each nucleotide along with the sequence (full name). Names used in bioruby are found in the Bio::AminoAcid::NAMES hash.

s = Bio::Sequence::NA.new('atg')
puts s.names                    #=> ["Adenine", "Thymine", "Guanine"]
Returns

Array object



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# File 'lib/bio/sequence/na.rb', line 407

def names
  array = []
  self.each_byte do |x|
    array.push(Bio::NucleicAcid.names[x.chr.upcase])
  end
  return array
end

#pikachu ⇒ Object

:nodoc:



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# File 'lib/bio/sequence/compat.rb', line 86

def pikachu #:nodoc:
  self.dna.tr("atgc", "pika") # joke, of course :-)
end

#reverse_complement ⇒ Object Also known as: complement

Returns a new sequence object with the reverse complement sequence to the original. The original sequence is not modified.

s = Bio::Sequence::NA.new('atgc')
puts s.reverse_complement               #=> 'gcat'
puts s                                  #=> 'atgc'
Returns

new Bio::Sequence::NA object



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# File 'lib/bio/sequence/na.rb', line 131

def reverse_complement
  s = self.class.new(self)
  s.reverse_complement!
  s
end

#reverse_complement! ⇒ Object Also known as: complement!

Converts the original sequence into its reverse complement.

The original sequence is modified.

s = Bio::Sequence::NA.new('atgc')
puts s.reverse_complement               #=> 'gcat'
puts s                                  #=> 'gcat'
Returns

current Bio::Sequence::NA object (modified)



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# File 'lib/bio/sequence/na.rb', line 145

def reverse_complement!
  self.reverse!
  self.forward_complement!
end

#rna ⇒ Object

Returns a new sequence object with any ‘t’ bases changed to ‘u’. The original sequence is not modified.

s = Bio::Sequence::NA.new('atgc')
puts s.dna                              #=> 'augc'  
puts s                                  #=> 'atgc'
Returns

new Bio::Sequence::NA object



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# File 'lib/bio/sequence/na.rb', line 447

def rna
  self.tr('t', 'u')
end

#rna! ⇒ Object

Changes any ‘t’ bases in the original sequence to ‘u’. The original sequence is modified.

s = Bio::Sequence::NA.new('atgc')
puts s.dna!                             #=> 'augc'
puts s                                  #=> 'augc'
Returns

current Bio::Sequence::NA object (modified)



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# File 'lib/bio/sequence/na.rb', line 459

def rna!
  self.tr!('t', 'u')
end

#splicing(position) ⇒ Object

Alias of Bio::Sequence::Common splice method, documented there.



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# File 'lib/bio/sequence/na.rb', line 82

def splicing(position) #:nodoc:
  mRNA = super
  if mRNA.rna?
    mRNA.tr!('t', 'u')
  else
    mRNA.tr!('u', 't')
  end
  mRNA
end

#to_midi(style = {}, drum = true) ⇒ Object

style:

Hash of :tempo, :scale, :tones

scale:

C  C# D  D# E  F  F# G  G# A  A#  B
0  1  2  3  4  5  6  7  8  9  10  11

tones:

Hash of :prog, :base, :range -- tone, vol? or len?, octaves

drum:

true (with rhythm part), false (without rhythm part)



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# File 'lib/bio/shell/plugin/midi.rb', line 351

def to_midi(style = {}, drum = true)
  default = MidiTrack::Styles["Ichinose"]
  if style.is_a?(String)
    style = MidiTrack::Styles[style] || default
  end
  tempo = style[:tempo] || default[:tempo]
  scale = style[:scale] || default[:scale]
  tones = style[:tones] || default[:tones]

  track = []

  tones.each_with_index do |tone, i|
    ch = i
    ch += 1 if i >= 9         # skip rythm track
    track.push MidiTrack.new(ch, tone[:prog], tone[:base], tone[:range], scale)
  end

  if drum
    rhythm = [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11]
    track.push(MidiTrack.new(9, 0, 35, 2, rhythm))
  end

  cur = 0
  window_search(4) do |s|
    track[cur % track.length].push(s)
    cur += 1
  end

  track.each do |t|
    t.push_silent(12)
  end

  ans = track[0].header(track.length, tempo)
  track.each do |t|
    ans += t.encode
  end
  return ans
end

#to_re ⇒ Object

Create a ruby regular expression instance (Regexp)

s = Bio::Sequence::NA.new('atggcgtga')
puts s.to_re                            #=> /atggcgtga/
Returns

Regexp object



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# File 'lib/bio/sequence/na.rb', line 391

def to_re
  if self.rna?
    Bio::NucleicAcid.to_re(self.dna, true)
  else
    Bio::NucleicAcid.to_re(self)
  end
end

#translate(frame = 1, table = 1, unknown = 'X') ⇒ Object

Translate into an amino acid sequence.

s = Bio::Sequence::NA.new('atggcgtga')
puts s.translate                        #=> "MA*"

By default, translate starts in reading frame position 1, but you can start in either 2 or 3 as well,

puts s.translate(2)                     #=> "WR"
puts s.translate(3)                     #=> "GV"

You may also translate the reverse complement in one step by using frame values of -1, -2, and -3 (or 4, 5, and 6)

puts s.translate(-1)                    #=> "SRH"
puts s.translate(4)                     #=> "SRH"
puts s.reverse_complement.translate(1)  #=> "SRH"

The default codon table in the translate function is the Standard Eukaryotic codon table. The translate function takes either a number or a Bio::CodonTable object for its table argument. The available tables are (NCBI):

1. "Standard (Eukaryote)"
2. "Vertebrate Mitochondrial"
3. "Yeast Mitochondorial"
4. "Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma"
5. "Invertebrate Mitochondrial"
6. "Ciliate Macronuclear and Dasycladacean"
9. "Echinoderm Mitochondrial"
10. "Euplotid Nuclear"
11. "Bacteria"
12. "Alternative Yeast Nuclear"
13. "Ascidian Mitochondrial"
14. "Flatworm Mitochondrial"
15. "Blepharisma Macronuclear"
16. "Chlorophycean Mitochondrial"
21. "Trematode Mitochondrial"
22. "Scenedesmus obliquus mitochondrial"
23. "Thraustochytrium Mitochondrial"

If you are using anything other than the default table, you must specify frame in the translate method call,

puts s.translate                #=> "MA*"  (using defaults)
puts s.translate(1,1)           #=> "MA*"  (same as above, but explicit)
puts s.translate(1,2)           #=> "MAW"  (different codon table)

and using a Bio::CodonTable instance in the translate method call,

mt_table = Bio::CodonTable[2]
puts s.translate(1, mt_table)           #=> "MAW"

By default, any invalid or unknown codons (as could happen if the sequence contains ambiguities) will be represented by ‘X’ in the translated sequence. You may change this to any character of your choice.

s = Bio::Sequence::NA.new('atgcNNtga')
puts s.translate                        #=> "MX*"
puts s.translate(1,1,'9')               #=> "M9*"

The translate method considers gaps to be unknown characters and treats them as such (i.e. does not collapse sequences prior to translation), so

s = Bio::Sequence::NA.new('atgc--tga')
puts s.translate                        #=> "MX*"

Arguments:

  • (optional) frame: one of 1,2,3,4,5,6,-1,-2,-3 (default 1)

  • (optional) table: Fixnum in range 1,23 or Bio::CodonTable object (default 1)

  • (optional) unknown: Character (default ‘X’)

Returns

Bio::Sequence::AA object



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# File 'lib/bio/sequence/na.rb', line 232

def translate(frame = 1, table = 1, unknown = 'X')
  if table.is_a?(Bio::CodonTable)
    ct = table
  else
    ct = Bio::CodonTable[table]
  end
  naseq = self.dna
  case frame
  when 1, 2, 3
    from = frame - 1
  when 4, 5, 6
    from = frame - 4
    naseq.complement!
  when -1, -2, -3
    from = -1 - frame
    naseq.complement!
  else
    from = 0
  end
  nalen = naseq.length - from
  nalen -= nalen % 3
  aaseq = naseq[from, nalen].gsub(/.{3}/) {|codon| ct[codon] or unknown}
  return Bio::Sequence::AA.new(aaseq)
end