X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=code_ruby%2Flib%2Fmaasha%2Fseq.rb;h=2788e5dcc02d78cdb9e3fd38ef83749bad158b79;hb=740804b81930af277b29c64f8b8276daff633f44;hp=2382218d1f91f4de415e25c58869b239a368deda;hpb=acc00ae480f88bfd38b1ebd60cae966130c3ddeb;p=biopieces.git

diff --git a/code_ruby/lib/maasha/seq.rb b/code_ruby/lib/maasha/seq.rb
index 2382218..2788e5d 100644
--- a/code_ruby/lib/maasha/seq.rb
+++ b/code_ruby/lib/maasha/seq.rb
@@ -22,12 +22,14 @@
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
-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.rb'
+autoload :Dynamic,     'maasha/seq/dynamic.rb'
+autoload :Homopolymer, 'maasha/seq/homopolymer.rb'
 
 # Residue alphabets
 DNA     = %w[a t c g]
@@ -35,19 +37,49 @@ 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[. - _ ~]
 
-# 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
 
@@ -56,7 +88,7 @@ class Seq
   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)
@@ -67,9 +99,9 @@ class Seq
     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
@@ -109,9 +141,9 @@ class Seq
     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
 
@@ -119,6 +151,7 @@ class Seq
   # by inspecting the first 100 residues.
   def type_guess!
     self.type = self.type_guess
+    self
   end
 
   # Returns the length of a sequence.
@@ -158,24 +191,24 @@ class Seq
 
   # 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
 
@@ -183,11 +216,60 @@ class Seq
   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?
@@ -253,17 +335,13 @@ class Seq
     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
@@ -273,6 +351,26 @@ class Seq
   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?
@@ -280,6 +378,8 @@ class Seq
     else
       raise SeqError, "Cannot complement sequence type: #{self.type}"
     end
+
+    self
   end
 
   # Method to determine the Hamming Distance between
@@ -292,55 +392,103 @@ class Seq
   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
@@ -355,40 +503,6 @@ 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_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.
@@ -402,23 +516,6 @@ class Seq
     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
@@ -431,21 +528,6 @@ class Seq
     ((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)
@@ -484,39 +566,112 @@ class Seq
     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__