| Module | Bio::Sequence::Common |
| In: |
lib/bio/sequence/compat.rb
lib/bio/sequence/common.rb |
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.
# 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
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 |
# File lib/bio/sequence/common.rb, line 121
121: def +(*arg)
122: self.class.new(super(*arg))
123: 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 |
# 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) |
# 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) |
# 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:
| Returns: | new Bio::Sequence::NA/AA object |
# 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 |
# File lib/bio/sequence/common.rb, line 65
65: def seq
66: self.class.new(self)
67: end
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 |
# 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
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:
| Returns: | new Bio::Sequence::NA/AA object |
# 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
DEPRECIATED Do not use! Use Bio::Sequence#output instead.
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:
| Returns: | String |
# File lib/bio/sequence/compat.rb, line 50
50: def to_fasta(header = '', width = nil)
51: warn "Bio::Sequence#to_fasta is obsolete. Use Bio::Sequence#output(:fasta) instead" if $DEBUG
52: ">#{header}\n" +
53: if width
54: self.to_s.gsub(Regexp.new(".{1,#{width}}"), "\\0\n")
55: else
56: self.to_s + "\n"
57: end
58: 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 |
# File lib/bio/sequence/common.rb, line 52
52: def to_s
53: String.new(self)
54: end
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:
| Returns: | Float object |
# 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:
| Returns: | new Bio::Sequence::NA/AA object |
# 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