module Bio::Sequence::Common
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
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
# File lib/bio/sequence/common.rb 121 def +(*arg) 122 self.class.new(super(*arg)) 123 end
# File lib/bio/sequence/common.rb 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
# File lib/bio/sequence/common.rb 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 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 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
# File lib/bio/sequence/common.rb 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 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:
-
(required) position: String or
Bio::Location
object
- Returns
-
Bio::Sequence::NA
/AA object
# File lib/bio/sequence/common.rb 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
Acts almost the same as String#split.
# File lib/bio/sequence/common.rb 311 def split(*arg) 312 if block_given? 313 super 314 else 315 ret = super(*arg) 316 ret.collect! { |x| self.class.new('').replace(x) } 317 ret 318 end 319 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:
-
(optional) s(start): Integer (default 1)
-
(optional) e(end): Integer (default current sequence length)
- Returns
-
new
Bio::Sequence::NA
/AA object
# File lib/bio/sequence/common.rb 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 DEPRECATED 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
# File lib/bio/sequence/compat.rb 49 def to_fasta(header = '', width = nil) 50 warn "Bio::Sequence#to_fasta is obsolete. Use Bio::Sequence#output(:fasta) instead" if $DEBUG 51 ">#{header}\n" + 52 if width 53 self.to_s.gsub(Regexp.new(".{1,#{width}}"), "\\0\n") 54 else 55 self.to_s + "\n" 56 end 57 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 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:
-
(required) hash: Hash object
- Returns
-
Float object
# File lib/bio/sequence/common.rb 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
# File lib/bio/sequence/common.rb 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