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

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

[Source]

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

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

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 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

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

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!

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:

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

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

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

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

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

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]