From 93cdd1c3b5b94db85707fbffe84be90095cce1b4 Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Tue, 7 Aug 2012 17:50:02 +0000
Subject: [PATCH] last fix on prodigal upgrade

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1888 74ccb610-7750-0410-82ae-013aeee3265d
---
 code_ruby/lib/maasha/prodigal.rb |  2 +-
 code_ruby/lib/maasha/seq.rb      | 81 ++++++++++++++++++++++++++++++++
 2 files changed, 82 insertions(+), 1 deletion(-)

diff --git a/code_ruby/lib/maasha/prodigal.rb b/code_ruby/lib/maasha/prodigal.rb
index 5fc0354..74e5bde 100644
--- a/code_ruby/lib/maasha/prodigal.rb
+++ b/code_ruby/lib/maasha/prodigal.rb
@@ -60,7 +60,7 @@ class Prodigal
         fields = entry.seq_name.split(" # ")
 
         record[:REC_TYPE] = "GENE"
-        record[:SEQ_NAME] = fields[0]
+        record[:S_ID]     = fields[0]
         record[:S_BEG]    = fields[1].to_i - 1
         record[:S_END]    = fields[2].to_i - 1
         record[:S_LEN]    = record[:S_END] - record[:S_BEG] + 1
diff --git a/code_ruby/lib/maasha/seq.rb b/code_ruby/lib/maasha/seq.rb
index 92d3398..b919a7f 100644
--- a/code_ruby/lib/maasha/seq.rb
+++ b/code_ruby/lib/maasha/seq.rb
@@ -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
@@ -190,6 +221,56 @@ 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?
-- 
2.39.5