# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
require 'maasha/bits'
-require 'maasha/seq/backtrack'
require 'maasha/seq/digest'
-#require 'maasha/seq/patscan'
-require 'maasha/seq/patternmatcher'
require 'maasha/seq/trim'
require 'narray'
+autoload :BackTrack, 'maasha/seq/backtrack.rb'
+autoload :Dynamic, 'maasha/seq/dynamic.rb'
+
# Residue alphabets
DNA = %w[a t c g]
RNA = %w[a u c g]
"GTG" => "V", "GCG" => "A", "GAG" => "E", "GGG" => "G"
}
-# Quality scores bases
-SCORE_BASE = 64
-SCORE_MIN = 0
-SCORE_MAX = 40
# Error class for all exceptions to do with Seq.
class SeqError < StandardError; end
class Seq
- #include Patscan
- include PatternMatcher
- include BackTrack
+ # Quality scores bases
+ SCORE_BASE = 33
+ SCORE_MIN = 0
+ SCORE_MAX = 40
+
include Digest
include Trim
# by inspecting the first 100 residues.
def type_guess!
self.type = self.type_guess
+ self
end
# Returns the length of a sequence.
key
end
- # Method to reverse complement sequence.
- def reverse_complement
- self.reverse
- self.complement
- self
+ # Method to reverse the sequence.
+ def reverse
+ Seq.new(self.seq_name, self.seq.reverse, self.type, self.qual ? self.qual.reverse : self.qual)
end
- alias :revcomp :reverse_complement
-
# Method to reverse the sequence.
- def reverse
+ def reverse!
self.seq.reverse!
self.qual.reverse! if self.qual
self
def complement
raise SeqError, "Cannot complement 0 length sequence" if self.length == 0
+ entry = Seq.new
+ entry.seq_name = self.seq_name
+ entry.type = self.type
+ entry.qual = self.qual
+
+ if self.is_dna?
+ entry.seq = self.seq.tr('AGCUTRYWSMKHDVBNagcutrywsmkhdvbn', 'TCGAAYRWSKMDHBVNtcgaayrwskmdhbvn')
+ elsif self.is_rna?
+ entry.seq = self.seq.tr('AGCUTRYWSMKHDVBNagcutrywsmkhdvbn', 'UCGAAYRWSKMDHBVNucgaayrwskmdhbvn')
+ else
+ raise SeqError, "Cannot complement sequence type: #{self.type}"
+ end
+
+ entry
+ end
+
+ # Method that complements sequence including ambiguity codes.
+ def complement!
+ raise SeqError, "Cannot complement 0 length sequence" if self.length == 0
+
if self.is_dna?
self.seq.tr!('AGCUTRYWSMKHDVBNagcutrywsmkhdvbn', 'TCGAAYRWSKMDHBVNtcgaayrwskmdhbvn')
elsif self.is_rna?
else
raise SeqError, "Cannot complement sequence type: #{self.type}"
end
+
+ self
end
# Method to determine the Hamming Distance between
seq_new
end
- # Method to shuffle a sequence readomly inline.
+ # Method to return a new Seq object with shuffled sequence.
+ def shuffle
+ Seq.new(self.seq_name, self.seq.split('').shuffle!.join, self.type, self.qual)
+ end
+
+ # Method to shuffle a sequence randomly inline.
def shuffle!
self.seq = self.seq.split('').shuffle!.join
self
end
+ # Method to concatenate sequence entries.
+ def <<(entry)
+ raise SeqError, "sequences of different types" unless self.type == entry.type
+ raise SeqError, "qual is missing in one entry" unless self.qual.class == entry.qual.class
+
+ self.seq << entry.seq
+ self.qual << entry.qual unless entry.qual.nil?
+
+ self
+ end
+
# Method that returns a subsequence of from a given start position
# and of a given length.
def subseq(start, length = self.length - start)
qual = self.qual[start .. stop] unless self.qual.nil?
end
- Seq.new(self.seq_name.dup, seq, self.type, qual)
+ Seq.new(self.seq_name, seq, self.type, qual) # TODO changed self.seq_name.dup to self.seq_name -> consequence?
end
# Method that replaces a sequence with a subsequence from a given start position
# and of a given length.
def subseq!(start, length = self.length - start)
- raise SeqError, "subsequence start: #{start} < 0" if start < 0
- raise SeqError, "subsequence length: #{length} < 0" if length < 0
- raise SeqError, "subsequence start + length > Seq.length: #{start} + #{length} > #{self.length}" if start + length > self.length
-
- if length == 0
- self.seq = ""
- self.qual = "" unless self.qual.nil?
- else
- stop = start + length - 1
+ s = subseq(start, length)
- self.seq = self.seq[start .. stop]
- self.qual = self.qual[start .. stop] unless self.qual.nil?
- end
+ self.seq_name = s.seq_name
+ self.seq = s.seq
+ self.type = s.type
+ self.qual = s.qual
self
end
((self.seq.scan(/[a-z]/).size.to_f / (self.len - self.indels).to_f) * 100).round(2)
end
- # Hard masks sequence residues where the corresponding quality score
- # is below a given cutoff.
- def mask_seq_hard_old(cutoff)
- seq = self.seq.upcase
- scores = self.qual
- i = 0
-
- scores.each_char do |score|
- seq[i] = 'N' if score.ord - SCORE_BASE < cutoff
- i += 1
- end
-
- self.seq = seq
- end
-
# Hard masks sequence residues where the corresponding quality score
# is below a given cutoff.
def mask_seq_hard!(cutoff)
self
end
- # Method to convert quality scores inbetween formats.
- # Sanger base 33, range 0-40
- # Solexa base 64, range -5-40
- # Illumina13 base 64, range 0-40
- # Illumina15 base 64, range 3-40
- # Illumina18 base 33, range 0-41
- def convert_scores!(from, to)
- unless from == to
- na_qual = NArray.to_na(self.qual, "byte")
+ # Method that determines if a quality score string can be
+ # absolutely identified as base 33.
+ def qual_base33?
+ self.qual.match(/[!-:]/) ? true : false
+ end
+
+ # Method that determines if a quality score string may be base 64.
+ def qual_base64?
+ self.qual.match(/[K-h]/) ? true : false
+ end
- case from.downcase
- when "sanger" then na_qual -= 33
- when "solexa" then na_qual -= 64
- when "illumina13" then na_qual -= 64
- when "illumina15" then na_qual -= 64
- when "illumina18" then na_qual -= 33
- else raise SeqError, "unknown quality score encoding: #{from}"
- end
+ # Method to determine if a quality score is valid accepting only 0-40 range.
+ def qual_valid?(encoding)
+ raise SeqError, "Missing qual" if self.qual.nil?
- case to.downcase
- when "sanger" then na_qual += 33
- when "solexa" then na_qual += 64
- when "illumina13" then na_qual += 64
- when "illumina15" then na_qual += 64
- when "illumina18" then na_qual += 33
- else raise SeqError, "unknown quality score encoding: #{from}"
- end
+ case encoding
+ when :base_33 then return true if self.qual.match(/^[!-I]*$/)
+ when :base_64 then return true if self.qual.match(/^[@-h]*$/)
+ else raise SeqError, "unknown quality score encoding: #{encoding}"
+ end
+
+ false
+ end
+
+ # Method to coerce quality scores to be within the 0-40 range.
+ def qual_coerce!(encoding)
+ raise SeqError, "Missing qual" if self.qual.nil?
+ case encoding
+ when :base_33 then self.qual.tr!("[J-~]", "I")
+ when :base_64 then self.qual.tr!("[i-~]", "h")
+ else raise SeqError, "unknown quality score encoding: #{encoding}"
+ end
+
+ self
+ end
+
+ # Method to convert quality scores.
+ def qual_convert!(from, to)
+ raise SeqError, "unknown quality score encoding: #{from}" unless from == :base_33 or from == :base_64
+ raise SeqError, "unknown quality score encoding: #{to}" unless to == :base_33 or to == :base_64
+
+ if from == :base_33 and to == :base_64
+ na_qual = NArray.to_na(self.qual, "byte")
+ na_qual += 64 - 33
+ self.qual = na_qual.to_s
+ elsif from == :base_64 and to == :base_33
+ self.qual.tr!("[;-?]", "@") # Handle negative Solexa values from -5 to -1 (set these to 0).
+ na_qual = NArray.to_na(self.qual, "byte")
+ na_qual -= 64 - 33
self.qual = na_qual.to_s
end
na_qual = NArray.to_na(self.qual, "byte")
na_qual -= SCORE_BASE
+
na_qual.mean
end
projects / biopieces.git / blobdiff