# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-require 'maasha/patternmatcher'
require 'maasha/bits'
-require 'maasha/backtrack'
-require 'maasha/digest'
+require 'maasha/seq/backtrack'
+require 'maasha/seq/digest'
+#require 'maasha/seq/patscan'
+require 'maasha/seq/patternmatcher'
+require 'maasha/seq/trim'
require 'narray'
-#require 'maasha/patscan'
# Residue alphabets
DNA = %w[a t c g]
INDELS = %w[. - _ ~]
# Quality scores bases
-SCORE_PHRED = 33
-SCORE_ILLUMINA = 64
-SCORE_MIN = 0
-SCORE_MAX = 40
+SCORE_BASE = 64
+SCORE_MIN = 0
+SCORE_MAX = 40
# Error class for all exceptions to do with Seq.
class SeqError < StandardError; end
include PatternMatcher
include BackTrack
include Digest
+ include Trim
attr_accessor :seq_name, :seq, :type, :qual
# 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} < 1" if length <= 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
- stop = start + length - 1
+ if length == 0
+ seq = ""
+ qual = "" unless self.qual.nil?
+ else
+ stop = start + length - 1
- seq = self.seq[start .. stop]
- qual = self.qual[start .. stop] unless self.qual.nil?
+ seq = self.seq[start .. stop]
+ qual = self.qual[start .. stop] unless self.qual.nil?
+ end
- Seq.new(self.seq_name, seq, self.type, qual)
+ Seq.new(self.seq_name.dup, seq, self.type, qual)
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} < 1" if length <= 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
- stop = start + length - 1
+ if length == 0
+ self.seq = ""
+ self.qual = "" unless self.qual.nil?
+ else
+ stop = start + length - 1
+
+ self.seq = self.seq[start .. stop]
+ self.qual = self.qual[start .. stop] unless self.qual.nil?
+ end
- self.seq = self.seq[start .. stop]
- self.qual = self.qual[start .. stop] unless self.qual.nil?
+ self
end
# Method that returns a subsequence of a given length
self.subseq(start, length)
end
- def quality_trim_right(min)
- raise SeqError, "no sequence" if self.seq.nil?
- raise SeqError, "no quality score" if self.qual.nil?
- raise SeqError, "minimum value: #{min} out of range #{SCORE_MIN} .. #{SCORE_MAX}" unless (SCORE_MIN .. SCORE_MAX).include? min
-
- regex_right = Regexp.new("[#{(SCORE_ILLUMINA).chr}-#{(SCORE_ILLUMINA + min).chr}]+$")
-
- self.qual.match(regex_right) do |m|
- self.subseq!(0, $`.length) if $`.length > 0
- end
-
- self
- end
-
- def quality_trim_left(min)
- raise SeqError, "no sequence" if self.seq.nil?
- raise SeqError, "no quality score" if self.qual.nil?
- raise SeqError, "minimum value: #{min} out of range #{SCORE_MIN} .. #{SCORE_MAX}" unless (SCORE_MIN .. SCORE_MAX).include? min
-
- regex_left = Regexp.new("^[#{(SCORE_ILLUMINA).chr}-#{(SCORE_ILLUMINA + min).chr}]+")
-
- self.qual.match(regex_left) do |m|
- self.subseq!(m.to_s.length, self.length - m.to_s.length) if self.length - m.to_s.length > 0
- end
-
- self
- end
-
- def quality_trim(min)
- self.quality_trim_right(min)
- self.quality_trim_left(min)
- self
- end
-
# Method that returns the residue compositions of a sequence in
# a hash where the key is the residue and the value is the residue
# count.
i = 0
scores.each_char do |score|
- seq[i] = 'N' if score.ord - SCORE_ILLUMINA < cutoff
+ seq[i] = 'N' if score.ord - SCORE_BASE < cutoff
i += 1
end
na_seq = NArray.to_na(self.seq, "byte")
na_qual = NArray.to_na(self.qual, "byte")
- mask = (na_qual - SCORE_ILLUMINA) < cutoff
+ mask = (na_qual - SCORE_BASE) < cutoff
+ mask *= na_seq.ne("-".ord)
na_seq[mask] = 'N'.ord
na_seq = NArray.to_na(self.seq, "byte")
na_qual = NArray.to_na(self.qual, "byte")
- mask = (na_qual - SCORE_ILLUMINA) < cutoff
+ mask = (na_qual - SCORE_BASE) < cutoff
+ mask *= na_seq.ne("-".ord)
na_seq[mask] ^= ' '.ord
self
end
- # Method to convert the quality scores from a specified base
- # to another base.
- def convert_phred2illumina!
- self.qual.gsub!(/./) do |score|
- score_phred = score.ord - SCORE_PHRED
- raise SeqError, "Bad Phred score: #{score} (#{score_phred})" unless (0 .. 41).include? score_phred
- score_illumina = score_phred + SCORE_ILLUMINA
- score = score_illumina.chr
- end
- 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")
+
+ 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
+
+ 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
- # Method to convert the quality scores from Solexa odd/ratio to
- # Illumina format.
- def convert_solexa2illumina!
- self.qual.gsub!(/./) do |score|
- score = solexa_char2illumina_char(score)
+ self.qual = na_qual.to_s
end
+
+ self
end
- private
+ # Method to calculate and return the mean quality score.
+ def scores_mean
+ raise SeqError, "Missing qual in entry" if self.qual.nil?
- # Method to convert a Solexa score (odd ratio) to
- # a phred (probability) integer score.
- def solexa2phred(score)
- (10.0 * Math.log(10.0 ** (score / 10.0) + 1.0, 10)).to_i
+ na_qual = NArray.to_na(self.qual, "byte")
+ na_qual -= SCORE_BASE
+ na_qual.mean
end
- # Method to convert a Solexa score encoded using base
- # 64 ASCII to a Phred score encoded using base 64 ASCII.
- def solexa_char2illumina_char(char)
- score_solexa = char.ord - 64
- score_phred = solexa2phred(score_solexa)
- (score_phred + 64).chr
+ # Method to find open reading frames (ORFs).
+ def each_orf(size_min, size_max, start_codons, stop_codons, pick_longest = false)
+ orfs = []
+ pos_beg = 0
+
+ regex_start = Regexp.new(start_codons.join('|'), true)
+ regex_stop = Regexp.new(stop_codons.join('|'), true)
+
+ while pos_beg and pos_beg < self.length - size_min
+ if pos_beg = self.seq.index(regex_start, pos_beg)
+ if pos_end = self.seq.index(regex_stop, pos_beg)
+ length = (pos_end - pos_beg) + 3
+
+ if (length % 3) == 0
+ if size_min <= length and length <= size_max
+ subseq = self.subseq(pos_beg, length)
+
+ orfs << [subseq, pos_beg, pos_end + 3]
+ end
+ end
+ end
+
+ pos_beg += 1
+ end
+ end
+
+ if pick_longest
+ orf_hash = {}
+
+ orfs.each { |orf| orf_hash[orf.last] = orf unless orf_hash[orf.last] }
+
+ orfs = orf_hash.values
+ end
+
+ if block_given?
+ orfs.each { |orf| yield orf }
+ else
+ return orfs
+ end
end
end