Class | Bio::Sequence::NA
In: | lib/bio/sequence/compat.rb lib/bio/sequence/na.rb
Parent: | Object

# DESCRIPTION

Bio::Sequence::NA represents a bare Nucleic Acid sequence in bioruby.

# USAGE

      # Create a Nucleic Acid sequence.
      dna = Bio::Sequence.auto('atgcatgcATGCATGCAAAA')
      rna = Bio::Sequence.auto('augcaugcaugcaugcaaaa')

      # What are the names of all the bases?
      puts dna.names
      puts rna.names

      # What is the GC percentage?
      puts dna.gc_percent
      puts rna.gc_percent

      # What is the molecular weight?
      puts dna.molecular_weight
      puts rna.molecular_weight

      # What is the reverse complement?
      puts dna.reverse_complement
      puts dna.complement

      # Is this sequence DNA or RNA?
      puts dna.rna?

      # Translate my sequence (see method docs for many options)
      puts dna.translate
      puts rna.translate

### Methods

at_content at_skew codon_usage complement complement! cut_with_enzyme cut_with_enzymes dna dna! forward_complement forward_complement! gc_content gc_percent gc_skew illegal_bases molecular_weight names new randomize reverse_complement reverse_complement! rna rna! rna? to_re translate

### Included Modules

Bio::Sequence::Common

### Public Class methods

new(str)

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

[Source]

        # File lib/bio/sequence/na.rb, line 75
    75:   def initialize(str)
    76:     super
    77:     self.downcase!
    78:     self.tr!(" \t\n\r",'')
    79:   end

randomize(*arg, &block)

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

[Source]

        # File lib/bio/sequence/compat.rb, line 82
    82:   def self.randomize(*arg, &block)
    83:     self.new('').randomize(*arg, &block)
    84:   end

### Public Instance methods

at_content()

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

[Source]

         # File lib/bio/sequence/na.rb, line 317
    317:   def at_content
    318:     count = self.composition
    319:     at = count['a'] + count['t'] + count['u']
    320:     gc = count['g'] + count['c']
    321:     return 0.0 if at + gc == 0
    322:     return at.quo(at + gc)
    323:   end

at_skew()

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

[Source]

         # File lib/bio/sequence/na.rb, line 345
    345:   def at_skew
    346:     count = self.composition
    347:     a = count['a']
    348:     t = count['t'] + count['u']
    349:     return 0.0 if a + t == 0
    350:     return (a - t).quo(a + t)
    351:   end

codon_usage()

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

[Source]

         # File lib/bio/sequence/na.rb, line 273
    273:   def codon_usage
    274:     hash = Hash.new(0)
    275:     self.window_search(3, 3) do |codon|
    276:       hash[codon] += 1
    277:     end
    278:     return hash
    279:   end

complement()

Alias for reverse_complement

complement!()

Alias for reverse_complement!

cut_with_enzyme(*args)

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

[Source]

         # File lib/bio/sequence/na.rb, line 479
    479:   def cut_with_enzyme(*args)
    480:     Bio::RestrictionEnzyme::Analysis.cut(self, *args)
    481:   end

cut_with_enzymes(*args)

Alias for cut_with_enzyme

dna()

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

[Source]

         # File lib/bio/sequence/na.rb, line 423
    423:   def dna
    424:     self.tr('u', 't')
    425:   end

dna!()

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)

[Source]

         # File lib/bio/sequence/na.rb, line 435
    435:   def dna!
    436:     self.tr!('u', 't')
    437:   end

forward_complement()

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

[Source]

         # File lib/bio/sequence/na.rb, line 100
    100:   def forward_complement
    101:     s = self.class.new(self)
    102:     s.forward_complement!
    103:     s
    104:   end

forward_complement!()

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)

[Source]

         # File lib/bio/sequence/na.rb, line 114
    114:   def forward_complement!
    115:     if self.rna?
    116:       self.tr!('augcrymkdhvbswn', 'uacgyrkmhdbvswn')
    117:     else
    118:       self.tr!('atgcrymkdhvbswn', 'tacgyrkmhdbvswn')
    119:     end
    120:     self
    121:   end

gc_content()

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

[Source]

         # File lib/bio/sequence/na.rb, line 303
    303:   def gc_content
    304:     count = self.composition
    305:     at = count['a'] + count['t'] + count['u']
    306:     gc = count['g'] + count['c']
    307:     return 0.0 if at + gc == 0
    308:     return gc.quo(at + gc)
    309:   end

gc_percent()

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

[Source]

         # File lib/bio/sequence/na.rb, line 288
    288:   def gc_percent
    289:     count = self.composition
    290:     at = count['a'] + count['t'] + count['u']
    291:     gc = count['g'] + count['c']
    292:     return 0 if at + gc == 0
    293:     gc = 100 * gc / (at + gc)
    294:     return gc
    295:   end

gc_skew()

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

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

Returns: | Float

[Source]

         # File lib/bio/sequence/na.rb, line 331
    331:   def gc_skew
    332:     count = self.composition
    333:     g = count['g']
    334:     c = count['c']
    335:     return 0.0 if g + c == 0
    336:     return (g - c).quo(g + c)
    337:   end

illegal_bases()

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

[Source]

         # File lib/bio/sequence/na.rb, line 360
    360:   def illegal_bases
    361:     self.scan(/[^atgcu]/).sort.uniq
    362:   end

molecular_weight()

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

[Source]

         # File lib/bio/sequence/na.rb, line 376
    376:   def molecular_weight
    377:     if self.rna?
    378:       Bio::NucleicAcid.weight(self, true)
    379:     else
    380:       Bio::NucleicAcid.weight(self)
    381:     end
    382:   end

names()

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

[Source]

         # File lib/bio/sequence/na.rb, line 407
    407:   def names
    408:     array = []
    409:     self.each_byte do |x|
    410:       array.push(Bio::NucleicAcid.names[x.chr.upcase])
    411:     end
    412:     return array
    413:   end

reverse_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

[Source]

         # File lib/bio/sequence/na.rb, line 131
    131:   def reverse_complement
    132:     s = self.class.new(self)
    133:     s.reverse_complement!
    134:     s
    135:   end

reverse_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)

[Source]

         # File lib/bio/sequence/na.rb, line 145
    145:   def reverse_complement!
    146:     self.reverse!
    147:     self.forward_complement!
    148:   end

rna()

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

[Source]

         # File lib/bio/sequence/na.rb, line 447
    447:   def rna
    448:     self.tr('t', 'u')
    449:   end

rna!()

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)

[Source]

         # File lib/bio/sequence/na.rb, line 459
    459:   def rna!
    460:     self.tr!('t', 'u')
    461:   end

to_re()

Create a ruby regular expression instance (Regexp)

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

Returns: | Regexp object

[Source]

         # File lib/bio/sequence/na.rb, line 391
    391:   def to_re
    392:     if self.rna?
    393:       Bio::NucleicAcid.to_re(self.dna, true)
    394:     else
    395:       Bio::NucleicAcid.to_re(self)
    396:     end
    397:   end

translate(frame = 1, table = 1, unknown = 'X')

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

[Source]

         # File lib/bio/sequence/na.rb, line 232
    232:   def translate(frame = 1, table = 1, unknown = 'X')
    233:     if table.is_a?(Bio::CodonTable)
    234:       ct = table
    235:     else
    236:       ct = Bio::CodonTable[table]
    237:     end
    238:     naseq = self.dna
    239:     case frame
    240:     when 1, 2, 3
    241:       from = frame - 1
    242:     when 4, 5, 6
    243:       from = frame - 4
    244:       naseq.complement!
    245:     when -1, -2, -3
    246:       from = -1 - frame
    247:       naseq.complement!
    248:     else
    249:       from = 0
    250:     end
    251:     nalen = naseq.length - from
    252:     nalen -= nalen % 3
    253:     aaseq = naseq[from, nalen].gsub(/.{3}/) {|codon| ct[codon] or unknown}
    254:     return Bio::Sequence::AA.new(aaseq)
    255:   end

### Protected Instance methods

rna?()

[Source]

         # File lib/bio/sequence/na.rb, line 463
    463:   def rna?
    464:     self.index('u')
    465:   end

[Validate]