Module | Bio::Sequence::Common
In: | lib/bio/sequence/common.rb lib/bio/sequence/compat.rb

# DESCRIPTION

Bio::Sequence::Common is a Mixin implementing methods common to Bio::Sequence::AA and Bio::Sequence::NA. All of these methods are available to either Amino Acid or Nucleic Acid sequences, and by encapsulation are also available to Bio::Sequence objects.

# USAGE

      # Create a sequence
      dna = Bio::Sequence.auto('atgcatgcatgc')

      # Splice out a subsequence using a Genbank-style location string
      puts dna.splice('complement(1..4)')

      # What is the base composition?
      puts dna.composition

      # Create a random sequence with the composition of a current sequence
      puts dna.randomize

### Methods

+ << composition concat normalize! randomize seq seq! splice splicing subseq to_fasta to_s to_str total window_search

### Public Instance methods

+(*arg)

Create a new sequence by adding to an existing sequence. The existing sequence is not modified.

      s = Bio::Sequence::NA.new('atgc')
      s2 = s + 'atgc'
      puts s2                                 #=> "atgcatgc"
      puts s                                  #=> "atgc"

The new sequence is of the same class as the existing sequence if the new data was added to an existing sequence,

      puts s2.class == s.class                #=> true

but if an existing sequence is added to a String, the result is a String

      s3 = 'atgc' + s
      puts s3.class                           #=> String

Returns: | new Bio::Sequence::NA/AA or String object

[Source]

         # File lib/bio/sequence/common.rb, line 121
    121:   def +(*arg)
    122:     self.class.new(super(*arg))
    123:   end

<<(*arg)

[Source]

         # File lib/bio/sequence/common.rb, line 98
     98:   def <<(*arg)
     99:     concat(*arg)
    100:   end

composition()

Returns a hash of the occurrence counts for each residue or base.

      s = Bio::Sequence::NA.new('atgc')
      puts s.composition              #=> {"a"=>1, "c"=>1, "g"=>1, "t"=>1}

Returns: | Hash object

[Source]

         # File lib/bio/sequence/common.rb, line 215
    215:   def composition
    216:     count = Hash.new(0)
    217:     self.scan(/./) do |x|
    218:       count[x] += 1
    219:     end
    220:     return count
    221:   end

concat(*arg)

Add new data to the end of the current sequence. The original sequence is modified.

      s = Bio::Sequence::NA.new('atgc')
      s << 'atgc'
      puts s                                  #=> "atgcatgc"
      s << s
      puts s                                  #=> "atgcatgcatgcatgc"

Returns: | current Bio::Sequence::NA/AA object (modified)

[Source]

        # File lib/bio/sequence/common.rb, line 94
    94:   def concat(*arg)
    95:     super(self.class.new(*arg))
    96:   end

normalize!()

Normalize the current sequence, removing all whitespace and transforming all positions to uppercase if the sequence is AA or transforming all positions to lowercase if the sequence is NA. The original sequence is modified.

      s = Bio::Sequence::NA.new('atgc')
      s.normalize!

Returns: | current Bio::Sequence::NA/AA object (modified)

[Source]

        # File lib/bio/sequence/common.rb, line 78
    78:   def normalize!
    79:     initialize(self)
    80:     self
    81:   end

randomize(hash = nil) {|seq[i, 1]| ...}

Returns a randomized sequence. The default is to retain the same base/residue composition as the original. If a hash of base/residue counts is given, the new sequence will be based on that hash composition. If a block is given, each new randomly selected position will be passed into the block. In all cases, the original sequence is not modified.

      s = Bio::Sequence::NA.new('atgc')
      puts s.randomize                        #=> "tcag"  (for example)

      new_composition = {'a' => 2, 't' => 2}
      puts s.randomize(new_composition)       #=> "ttaa"  (for example)

      count = 0
      s.randomize { |x| count += 1 }
      puts count                              #=> 4

Arguments:

- (optional) hash: Hash object

Returns: | new Bio::Sequence::NA/AA object

[Source]

         # File lib/bio/sequence/common.rb, line 243
    243:   def randomize(hash = nil)
    244:     if hash
    245:       tmp = ''
    246:       hash.each {|k, v|
    247:         tmp += k * v.to_i
    248:       }
    249:     else
    250:       tmp = self
    251:     end
    252:     seq = self.class.new(tmp)
    253:     # Reference: http://en.wikipedia.org/wiki/Fisher-Yates_shuffle
    254:     seq.length.downto(2) do |n|
    255:       k = rand(n)
    256:       c = seq[n - 1]
    257:       seq[n - 1] = seq[k]
    258:       seq[k] = c
    259:     end
    260:     if block_given? then
    261:       (0...seq.length).each do |i|
    262:         yield seq[i, 1]
    263:       end
    264:       return self.class.new('')
    265:     else
    266:       return seq
    267:     end
    268:   end

seq()

Create a new sequence based on the current sequence. The original sequence is unchanged.

      s = Bio::Sequence::NA.new('atgc')
      s2 = s.seq
      puts s2                                 #=> 'atgc'

Returns: | new Bio::Sequence::NA/AA object

[Source]

        # File lib/bio/sequence/common.rb, line 65
    65:   def seq
    66:     self.class.new(self)
    67:   end

seq!()

Alias for normalize!

splice(position)

Return a new sequence extracted from the original using a GenBank style position string. See also documentation for the Bio::Location class.

      s = Bio::Sequence::NA.new('atgcatgcatgcatgc')
      puts s.splice('1..3')                           #=> "atg"
      puts s.splice('join(1..3,8..10)')               #=> "atgcat"
      puts s.splice('complement(1..3)')               #=> "cat"
      puts s.splice('complement(join(1..3,8..10))')   #=> "atgcat"

Note that ‘complement‘ed Genbank position strings will have no effect on Bio::Sequence::AA objects.

Arguments:

- (required) position: String or Bio::Location object

Returns: | Bio::Sequence::NA/AA object

[Source]

         # File lib/bio/sequence/common.rb, line 285
    285:   def splice(position)
    286:     unless position.is_a?(Locations) then
    287:       position = Locations.new(position)
    288:     end
    289:     s = ''
    290:     position.each do |location|
    291:       if location.sequence
    292:         s << location.sequence
    293:       else
    294:         exon = self.subseq(location.from, location.to)
    295:         begin
    296:           exon.complement! if location.strand < 0
    297:         rescue NameError
    298:         end
    299:         s << exon
    300:       end
    301:     end
    302:     return self.class.new(s)
    303:   end

splicing(position)

Alias for splice

subseq(s = 1, e = self.length)

Returns a new sequence containing the subsequence identified by the start and end numbers given as parameters. *Important:* Biological sequence numbering conventions (one-based) rather than ruby‘s (zero-based) numbering conventions are used.

      s = Bio::Sequence::NA.new('atggaatga')
      puts s.subseq(1,3)                      #=> "atg"

Start defaults to 1 and end defaults to the entire existing string, so subseq called without any parameters simply returns a new sequence identical to the existing sequence.

      puts s.subseq                           #=> "atggaatga"

Arguments:

- (optional) s(start): Integer (default 1)
- (optional) e(end): Integer (default current sequence length)

Returns: | new Bio::Sequence::NA/AA object

[Source]

         # File lib/bio/sequence/common.rb, line 143
    143:   def subseq(s = 1, e = self.length)
    144:     raise "Error: start/end position must be a positive integer" unless s > 0 and e > 0
    145:     s -= 1
    146:     e -= 1
    147:     self[s..e]
    148:   end

to_fasta(header = '', width = nil)

Bio::Sequence#to_fasta is DEPRECIATED Do not use Bio::Sequence#to_fasta ! Use Bio::Sequence#output instead. Note that Bio::Sequence::NA#to_fasta, Bio::Sequence::AA#to_fasata, and Bio::Sequence::Generic#to_fasta can still be used, because there are no alternative methods.

Output the FASTA format string of the sequence. The 1st argument is used as the comment string. If the 2nd option is given, the output sequence will be folded.

Arguments:

- (optional) header: String object
- (optional) width: Fixnum object (default nil)

Returns: | String

[Source]

        # File lib/bio/sequence/compat.rb, line 54
    54:   def to_fasta(header = '', width = nil)
    55:     warn "Bio::Sequence#to_fasta is obsolete. Use Bio::Sequence#output(:fasta) instead" if $DEBUG
    56:     ">#{header}\n" +
    57:     if width
    58:       self.to_s.gsub(Regexp.new(".{1,#{width}}"), "\\0\n")
    59:     else
    60:       self.to_s + "\n"
    61:     end
    62:   end

to_s()

Return sequence as String. The original sequence is unchanged.

      seq = Bio::Sequence::NA.new('atgc')
      puts s.to_s                             #=> 'atgc'
      puts s.to_s.class                       #=> String
      puts s                                  #=> 'atgc'
      puts s.class                            #=> Bio::Sequence::NA

Returns: | String object

[Source]

        # File lib/bio/sequence/common.rb, line 52
    52:   def to_s
    53:     String.new(self)
    54:   end

to_str()

Alias for to_s

total(hash)

Returns a float total value for the sequence given a hash of base or residue values,

      values = {'a' => 0.1, 't' => 0.2, 'g' => 0.3, 'c' => 0.4}
      s = Bio::Sequence::NA.new('atgc')
      puts s.total(values)                    #=> 1.0

Arguments:

- (required) hash: Hash object

Returns: | Float object

[Source]

         # File lib/bio/sequence/common.rb, line 198
    198:   def total(hash)
    199:     hash.default = 0.0 unless hash.default
    200:     sum = 0.0
    201:     self.each_byte do |x|
    202:       begin
    203:         sum += hash[x.chr]
    204:       end
    205:     end
    206:     return sum
    207:   end

window_search(window_size, step_size = 1) {|self[i, window_size]| ...}

This method steps through a sequences in steps of ‘step_size’ by subsequences of ‘window_size’. Typically used with a block. Any remaining sequence at the terminal end will be returned.

Prints average GC% on each 100bp

      s.window_search(100) do |subseq|
        puts subseq.gc
      end

Prints every translated peptide (length 5aa) in the same frame

      s.window_search(15, 3) do |subseq|
        puts subseq.translate
      end

Split genome sequence by 10000bp with 1000bp overlap in fasta format

      i = 1
      remainder = s.window_search(10000, 9000) do |subseq|
        puts subseq.to_fasta("segment #{i}", 60)
        i += 1
      end
      puts remainder.to_fasta("segment #{i}", 60)

Arguments:

- (required) window_size: Fixnum
- (optional) step_size: Fixnum (default 1)

Returns: | new Bio::Sequence::NA/AA object

[Source]

         # File lib/bio/sequence/common.rb, line 179
    179:   def window_search(window_size, step_size = 1)
    180:     last_step = 0
    181:     0.step(self.length - window_size, step_size) do |i|
    182:       yield self[i, window_size]
    183:       last_step = i
    184:     end
    185:     return self[last_step + window_size .. -1]
    186:   end

[Validate]