X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=code_ruby%2Flib%2Fmaasha%2Fseq.rb;h=f2d93d1fc5bbf86b6611e56e9eb9ce98d9185795;hb=d4b9c1bec954d5ff3e6eb2f7dc6c1aaa1f7f810f;hp=f4abff7c36aafba918a04b76d5e6f3544345225c;hpb=4228c538897ac3ce803984d5219473e890277b6e;p=biopieces.git

diff --git a/code_ruby/lib/maasha/seq.rb b/code_ruby/lib/maasha/seq.rb
index f4abff7..f2d93d1 100644
--- a/code_ruby/lib/maasha/seq.rb
+++ b/code_ruby/lib/maasha/seq.rb
@@ -22,11 +22,13 @@
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
-require 'maasha/patternmatcher'
 require 'maasha/bits'
-require 'maasha/backtrack'
-require 'maasha/digest'
-#require 'maasha/patscan'
+require 'maasha/seq/digest'
+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]
@@ -34,20 +36,48 @@ RNA     = %w[a u 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[. - _ ~]
 
+# 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"
+}
+
 # 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
 
 class Seq
-  #include Patscan
-  include PatternMatcher
-  include BackTrack
   include Digest
+  include Trim
 
   attr_accessor :seq_name, :seq, :type, :qual
 
@@ -188,6 +218,56 @@ class Seq
     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?
@@ -319,28 +399,33 @@ class Seq
   # 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, 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} < 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
@@ -355,40 +440,6 @@ class Seq
     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.
@@ -433,67 +484,171 @@ class Seq
 
   # Hard masks sequence residues where the corresponding quality score
   # is below a given cutoff.
-  def mask_seq_hard!(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_ILLUMINA < cutoff
+      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)
+    raise SeqError, "seq is nil"  if self.seq.nil?
+    raise SeqError, "qual is nil" if self.qual.nil?
+    raise SeqError, "cufoff value: #{cutoff} out of range #{SCORE_MIN} .. #{SCORE_MAX}" unless (SCORE_MIN .. SCORE_MAX).include? cutoff
+
+    na_seq  = NArray.to_na(self.seq, "byte")
+    na_qual = NArray.to_na(self.qual, "byte")
+    mask    = (na_qual - SCORE_BASE) < cutoff
+    mask   *= na_seq.ne("-".ord)
+
+    na_seq[mask] = 'N'.ord
+
+    self.seq = na_seq.to_s
+
+    self
+  end
+
   # Soft masks sequence residues where the corresponding quality score
   # is below a given cutoff.
   def mask_seq_soft!(cutoff)
-    seq    = self.seq.upcase
-    scores = self.qual
-    i      = 0
+    raise SeqError, "seq is nil"  if self.seq.nil?
+    raise SeqError, "qual is nil" if self.qual.nil?
+    raise SeqError, "cufoff value: #{cutoff} out of range #{SCORE_MIN} .. #{SCORE_MAX}" unless (SCORE_MIN .. SCORE_MAX).include? cutoff
 
-    scores.each_char do |score|
-      seq[i] = seq[i].downcase if score.ord - SCORE_ILLUMINA < cutoff
-      i += 1 
-    end
+    na_seq  = NArray.to_na(self.seq, "byte")
+    na_qual = NArray.to_na(self.qual, "byte")
+    mask    = (na_qual - SCORE_BASE) < cutoff
+    mask   *= na_seq.ne("-".ord)
 
-    self.seq = seq
+    na_seq[mask] ^= ' '.ord
+
+    self.seq = na_seq.to_s
+
+    self
+  end
+
+  # 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 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
+  # Method that determines if a quality score string can be
+  # absolutely identified as base 64.
+  def qual_base64?
+    self.qual.match(/[K-h]/) ? true : false
+  end
+
+  # Method to determine if a quality score is valid.
+  def qual_valid?(encoding)
+    raise SeqError, "Missing qual" if self.qual.nil?
+
+    case encoding.downcase
+    when "sanger"     then return true if self.qual.match(/^[!-I]*$/)
+    when "454"        then return true if self.qual.match(/^[@-h]*$/)
+    when "solexa"     then return true if self.qual.match(/^[;-h]*$/)
+    when "illumina13" then return true if self.qual.match(/^[@-h]*$/)
+    when "illumina15" then return true if self.qual.match(/^[@-h]*$/)
+    when "illumina18" then return true if self.qual.match(/^[!-J]*$/)
+    else raise SeqError, "unknown quality score encoding: #{encoding}"
     end
+
+    false
   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)
+  # Method to convert quality scores inbetween formats.
+  # Sanger     base 33, range  0-40 
+  # 454        base 64, range  0-40 
+  # Solexa     base 64, range -5-40 
+  # Illumina13 base 64, range  0-40 
+  # Illumina15 base 64, range  0-40 
+  # 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 "454"        then na_qual -= 64
+      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 "454"        then na_qual += 64
+      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: #{to}"
+      end
+
+      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