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 77
    77:   def initialize(str)
    78:     super
    79:     self.downcase!
    80:     self.tr!(" \t\n\r",'')
    81:   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 87
    87:   def self.randomize(*arg, &block)
    88:     self.new('').randomize(*arg, &block)
    89:   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 319
    319:   def at_content
    320:     count = self.composition
    321:     at = count['a'] + count['t'] + count['u']
    322:     gc = count['g'] + count['c']
    323:     return 0.0 if at + gc == 0
    324:     return at.quo(at + gc)
    325:   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 347
    347:   def at_skew
    348:     count = self.composition
    349:     a = count['a']
    350:     t = count['t'] + count['u']
    351:     return 0.0 if a + t == 0
    352:     return (a - t).quo(a + t)
    353:   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 275
    275:   def codon_usage
    276:     hash = Hash.new(0)
    277:     self.window_search(3, 3) do |codon|
    278:       hash[codon] += 1
    279:     end
    280:     return hash
    281:   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 481
    481:   def cut_with_enzyme(*args)
    482:     Bio::RestrictionEnzyme::Analysis.cut(self, *args)
    483:   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 425
    425:   def dna
    426:     self.tr('u', 't')
    427:   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 437
    437:   def dna!
    438:     self.tr!('u', 't')
    439:   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 102
    102:   def forward_complement
    103:     s = self.class.new(self)
    104:     s.forward_complement!
    105:     s
    106:   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 116
    116:   def forward_complement!
    117:     if self.rna?
    118:       self.tr!('augcrymkdhvbswn', 'uacgyrkmhdbvswn')
    119:     else
    120:       self.tr!('atgcrymkdhvbswn', 'tacgyrkmhdbvswn')
    121:     end
    122:     self
    123:   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 305
    305:   def gc_content
    306:     count = self.composition
    307:     at = count['a'] + count['t'] + count['u']
    308:     gc = count['g'] + count['c']
    309:     return 0.0 if at + gc == 0
    310:     return gc.quo(at + gc)
    311:   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 290
    290:   def gc_percent
    291:     count = self.composition
    292:     at = count['a'] + count['t'] + count['u']
    293:     gc = count['g'] + count['c']
    294:     return 0 if at + gc == 0
    295:     gc = 100 * gc / (at + gc)
    296:     return gc
    297:   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 333
    333:   def gc_skew
    334:     count = self.composition
    335:     g = count['g']
    336:     c = count['c']
    337:     return 0.0 if g + c == 0
    338:     return (g - c).quo(g + c)
    339:   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 362
    362:   def illegal_bases
    363:     self.scan(/[^atgcu]/).sort.uniq
    364:   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 378
    378:   def molecular_weight
    379:     if self.rna?
    380:       Bio::NucleicAcid.weight(self, true)
    381:     else
    382:       Bio::NucleicAcid.weight(self)
    383:     end
    384:   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 409
    409:   def names
    410:     array = []
    411:     self.each_byte do |x|
    412:       array.push(Bio::NucleicAcid.names[x.chr.upcase])
    413:     end
    414:     return array
    415:   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 133
    133:   def reverse_complement
    134:     s = self.class.new(self)
    135:     s.reverse_complement!
    136:     s
    137:   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 147
    147:   def reverse_complement!
    148:     self.reverse!
    149:     self.forward_complement!
    150:   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 449
    449:   def rna
    450:     self.tr('t', 'u')
    451:   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 461
    461:   def rna!
    462:     self.tr!('t', 'u')
    463:   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 393
    393:   def to_re
    394:     if self.rna?
    395:       Bio::NucleicAcid.to_re(self.dna, true)
    396:     else
    397:       Bio::NucleicAcid.to_re(self)
    398:     end
    399:   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 234
    234:   def translate(frame = 1, table = 1, unknown = 'X')
    235:     if table.is_a?(Bio::CodonTable)
    236:       ct = table
    237:     else
    238:       ct = Bio::CodonTable[table]
    239:     end
    240:     naseq = self.dna
    241:     case frame
    242:     when 1, 2, 3
    243:       from = frame - 1
    244:     when 4, 5, 6
    245:       from = frame - 4
    246:       naseq.complement!
    247:     when -1, -2, -3
    248:       from = -1 - frame
    249:       naseq.complement!
    250:     else
    251:       from = 0
    252:     end
    253:     nalen = naseq.length - from
    254:     nalen -= nalen % 3
    255:     aaseq = naseq[from, nalen].gsub(/.{3}/) {|codon| ct[codon] or unknown}
    256:     return Bio::Sequence::AA.new(aaseq)
    257:   end

### Protected Instance methods

rna?()

[Source]

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

[Validate]