X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=code_ruby%2Flib%2Fmaasha%2Fseq.rb;h=f2d93d1fc5bbf86b6611e56e9eb9ce98d9185795;hb=d4b9c1bec954d5ff3e6eb2f7dc6c1aaa1f7f810f;hp=b45540bace7491a881eded44e440f13c07c43b7c;hpb=37a8910b7465c8e6aeb2c8211f083f0a40ea2380;p=biopieces.git

diff --git a/code_ruby/lib/maasha/seq.rb b/code_ruby/lib/maasha/seq.rb
index b45540b..f2d93d1 100644
--- a/code_ruby/lib/maasha/seq.rb
+++ b/code_ruby/lib/maasha/seq.rb
@@ -22,13 +22,13 @@
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
-require 'maasha/patternmatcher'
 require 'maasha/bits'
-require 'maasha/backtrack'
 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'
 
 # Residue alphabets
 DNA     = %w[a t c g]
@@ -36,6 +36,37 @@ 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_BASE = 64
 SCORE_MIN  = 0
@@ -45,9 +76,6 @@ SCORE_MAX  = 40
 class SeqError < StandardError; end
 
 class Seq
-  #include Patscan
-  include PatternMatcher
-  include BackTrack
   include Digest
   include Trim
 
@@ -190,6 +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?
@@ -324,7 +402,6 @@ class Seq
     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
       seq  = ""
       qual = "" unless self.qual.nil?
@@ -335,26 +412,18 @@ class Seq
       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} < 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
@@ -466,11 +535,41 @@ class Seq
     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 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 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  3-40 
+  # Illumina15 base 64, range  0-40 
   # Illumina18 base 33, range  0-41 
   def convert_scores!(from, to)
     unless from == to
@@ -478,6 +577,7 @@ class Seq
 
       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
@@ -487,11 +587,12 @@ class Seq
 
       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: #{from}"
+      else raise SeqError, "unknown quality score encoding: #{to}"
       end
 
       self.qual = na_qual.to_s
@@ -499,6 +600,56 @@ class Seq
 
     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__