# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-require 'maasha/patternmatcher'
require 'maasha/bits'
-require 'maasha/backtrack'
-require 'maasha/digest'
+require 'maasha/seq/digest'
+require 'maasha/seq/trim'
require 'narray'
-#require 'maasha/patscan'
+
+autoload :BackTrack, 'maasha/seq/backtrack'
+autoload :Dynamic, 'maasha/seq/dynamic'
+autoload :Homopolymer, 'maasha/seq/homopolymer'
+autoload :Levenshtein, 'maasha/seq/levenshtein'
# Residue alphabets
DNA = %w[a t c g]
PROTEIN = %w[f l s y c w p h q r i m t n k v a d e g]
INDELS = %w[. - _ ~]
-# Quality scores bases
-SCORE_BASE = 64
-SCORE_MIN = 0
-SCORE_MAX = 40
+# Translation table 11
+# (http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes#SG11)
+# AAs = FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
+# Starts = ---M---------------M------------MMMM---------------M------------
+# Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+# Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+# Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+TRANS_TAB11_START = {
+ "TTG" => "M", "CTG" => "M", "ATT" => "M", "ATC" => "M",
+ "ATA" => "M", "ATG" => "M", "GTG" => "M"
+}
+
+TRANS_TAB11 = {
+ "TTT" => "F", "TCT" => "S", "TAT" => "Y", "TGT" => "C",
+ "TTC" => "F", "TCC" => "S", "TAC" => "Y", "TGC" => "C",
+ "TTA" => "L", "TCA" => "S", "TAA" => "*", "TGA" => "*",
+ "TTG" => "L", "TCG" => "S", "TAG" => "*", "TGG" => "W",
+ "CTT" => "L", "CCT" => "P", "CAT" => "H", "CGT" => "R",
+ "CTC" => "L", "CCC" => "P", "CAC" => "H", "CGC" => "R",
+ "CTA" => "L", "CCA" => "P", "CAA" => "Q", "CGA" => "R",
+ "CTG" => "L", "CCG" => "P", "CAG" => "Q", "CGG" => "R",
+ "ATT" => "I", "ACT" => "T", "AAT" => "N", "AGT" => "S",
+ "ATC" => "I", "ACC" => "T", "AAC" => "N", "AGC" => "S",
+ "ATA" => "I", "ACA" => "T", "AAA" => "K", "AGA" => "R",
+ "ATG" => "M", "ACG" => "T", "AAG" => "K", "AGG" => "R",
+ "GTT" => "V", "GCT" => "A", "GAT" => "D", "GGT" => "G",
+ "GTC" => "V", "GCC" => "A", "GAC" => "D", "GGC" => "G",
+ "GTA" => "V", "GCA" => "A", "GAA" => "E", "GGA" => "G",
+ "GTG" => "V", "GCG" => "A", "GAG" => "E", "GGG" => "G"
+}
# 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
attr_accessor :seq_name, :seq, :type, :qual
def self.new_bp(record)
seq_name = record[:SEQ_NAME]
seq = record[:SEQ]
- type = record[:SEQ_TYPE]
+ type = record[:SEQ_TYPE].to_sym if record[:SEQ_TYPE]
qual = record[:SCORES]
self.new(seq_name, seq, type, qual)
raise SeqError, "Cannot generate negative oligo length: #{length}" if length <= 0
case type.downcase
- when /dna/ then alph = DNA
- when /rna/ then alph = RNA
- when /protein/ then alph = PROTEIN
+ when :dna then alph = DNA
+ when :rna then alph = RNA
+ when :protein then alph = PROTEIN
else
raise SeqError, "Unknown sequence type: #{type}"
end
raise SeqError, "Guess failed: sequence is nil" if self.seq.nil?
case self.seq[0 ... 100].downcase
- when /[flpqie]/ then return "protein"
- when /[u]/ then return "rna"
- else return "dna"
+ when /[flpqie]/ then return :protein
+ when /[u]/ then return :rna
+ else return :dna
end
end
# by inspecting the first 100 residues.
def type_guess!
self.type = self.type_guess
+ self
end
# Returns the length of a sequence.
# Method that returns true is a given sequence type is DNA.
def is_dna?
- self.type == 'dna'
+ self.type == :dna
end
# Method that returns true is a given sequence type is RNA.
def is_rna?
- self.type == 'rna'
+ self.type == :rna
end
# Method that returns true is a given sequence type is protein.
def is_protein?
- self.type == 'protein'
+ self.type == :protein
end
# Method to transcribe DNA to RNA.
def to_rna
raise SeqError, "Cannot transcribe 0 length sequence" if self.length == 0
raise SeqError, "Cannot transcribe sequence type: #{self.type}" unless self.is_dna?
- self.type = 'rna'
+ self.type = :rna
self.seq.tr!('Tt','Uu')
end
def to_dna
raise SeqError, "Cannot reverse-transcribe 0 length sequence" if self.length == 0
raise SeqError, "Cannot reverse-transcribe sequence type: #{self.type}" unless self.is_rna?
-
- self.type = 'dna'
+ self.type = :dna
self.seq.tr!('Uu','Tt')
end
+ # Method to translate a DNA sequence to protein.
+ def translate!(trans_tab = 11)
+ raise SeqError, "Sequence type must be 'dna' - not #{self.type}" unless self.type == :dna
+ raise SeqError, "Sequence length must be a multiplum of 3 - was: #{self.length}" unless (self.length % 3) == 0
+
+ case trans_tab
+ when 11
+ codon_start_hash = TRANS_TAB11_START
+ codon_hash = TRANS_TAB11
+ else
+ raise SeqError, "Unknown translation table: #{trans_tab}"
+ end
+
+ codon = self.seq[0 ... 3].upcase
+
+ aa = codon_start_hash[codon]
+
+ raise SeqError, "Unknown start codon: #{codon}" if aa.nil?
+
+ protein = aa
+
+ i = 3
+
+ while i < self.length
+ codon = self.seq[i ... i + 3].upcase
+
+ aa = codon_hash[codon]
+
+ raise SeqError, "Unknown codon: #{codon}" if aa.nil?
+
+ protein << aa
+
+ i += 3
+ end
+
+ self.seq = protein
+ self.qual = nil
+ self.type = :protein
+
+ self
+ end
+
+ alias :to_protein! :translate!
+
+ def translate(trans_tab = 11)
+ self.dup.translate!(trans_tab)
+ end
+
+ alias :to_protein :translate
+
# Method that given a Seq entry returns a Biopieces record (a hash).
def to_bp
raise SeqError, "Missing seq_name" if self.seq_name.nil?
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
# two Sequence objects (case insensitive).
- def hamming_distance(seq)
- self.seq.upcase.hamming_distance(seq.seq.upcase)
+ def hamming_distance(entry)
+ self.seq.upcase.hamming_distance(entry.seq.upcase)
+ end
+
+ # Method to determine the Edit Distance between
+ # two Sequence objects (case insensitive).
+ def edit_distance(entry)
+ Levenshtein.distance(self.seq, entry.seq)
end
# Method that generates a random sequence of a given length and type.
def generate(length, type)
raise SeqError, "Cannot generate sequence length < 1: #{length}" if length <= 0
- case type.downcase
- when "dna"
- alph = DNA
- when "rna"
- alph = RNA
- when "protein"
- alph = PROTEIN
+ case type
+ when :dna then alph = DNA
+ when :rna then alph = RNA
+ when :protein then alph = PROTEIN
else
raise SeqError, "Unknown sequence type: #{type}"
end
seq_new = Array.new(length) { alph[rand(alph.size)] }.join("")
self.seq = seq_new
- self.type = type.downcase
+ self.type = type
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 add two Seq objects.
+ def +(entry)
+ new_entry = Seq.new()
+ new_entry.seq = self.seq + entry.seq
+ new_entry.type = self.type if self.type == entry.type
+ new_entry.qual = self.qual + entry.qual if self.qual and entry.qual
+ new_entry
+ 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
+
+ # Index method for Seq objects.
+ def [](*args)
+ entry = Seq.new
+ entry.seq_name = self.seq_name
+ entry.seq = self.seq[*args]
+ entry.type = self.type
+ entry.qual = self.qual[*args] unless self.qual.nil?
+
+ entry
+ end
+
+ # Index assignment method for Seq objects.
+ def []=(*args, entry)
+ self.seq[*args] = entry.seq[*args]
+ self.qual[*args] = entry.qual[*args] unless self.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)
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?
+ end
- seq = self.seq[start .. stop]
- qual = self.qual[start .. stop] unless self.qual.nil?
+ seq_name = self.seq_name.nil? ? nil : self.seq_name.dup
- Seq.new(self.seq_name, seq, self.type, qual)
+ Seq.new(seq_name, 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 start + length > Seq.length: #{start} + #{length} > #{self.length}" if start + length > self.length
+ s = subseq(start, length)
- stop = start + length - 1
+ self.seq_name = s.seq_name
+ self.seq = s.seq
+ self.type = s.type
+ self.qual = s.qual
- 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_BASE).chr}-#{(SCORE_BASE + 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_BASE).chr}-#{(SCORE_BASE + 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.
comp
end
- # Method that returns the length of the longest homopolymeric stretch
- # found in a sequence.
- def homopol_max(min = 1)
- return 0 if self.seq.nil? or self.seq.empty?
-
- found = false
-
- self.seq.upcase.scan(/A{#{min},}|T{#{min},}|G{#{min},}|C{#{min},}|N{#{min},}/) do |match|
- found = true
- min = match.size > min ? match.size : min
- end
-
- return 0 unless found
-
- min
- end
-
# Method that returns the percentage of hard masked residues
# or N's in a sequence.
def hard_mask
((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
self
end
+
+ # Method to calculate and return the mean quality score.
+ def scores_mean
+ raise SeqError, "Missing qual in entry" if self.qual.nil?
+
+ na_qual = NArray.to_na(self.qual, "byte")
+ na_qual -= SCORE_BASE
+
+ na_qual.mean
+ end
+
+ # 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
__END__
projects / biopieces.git / blobdiff