From b2cec0d7e409c133c2af442c861470a6d383b502 Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Tue, 12 Oct 2010 14:31:38 +0000
Subject: [PATCH] added solexa switch to read_fastq

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1110 74ccb610-7750-0410-82ae-013aeee3265d
---
 bp_bin/read_fastq            |  4 +++-
 bp_test/out/read_fastq.out.3 |  5 +++++
 bp_test/test/test_read_fastq |  4 ++++
 code_ruby/Maasha/lib/seq.rb  | 36 ++++++++++++++++++++++++++++++------
 4 files changed, 42 insertions(+), 7 deletions(-)
 create mode 100644 bp_test/out/read_fastq.out.3

diff --git a/bp_bin/read_fastq b/bp_bin/read_fastq
index cb114ff..fd88bf0 100755
--- a/bp_bin/read_fastq
+++ b/bp_bin/read_fastq
@@ -34,6 +34,7 @@ require 'fastq'
 casts = []
 casts << {:long=>'data_in', :short=>'i', :type=>'files!', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
 casts << {:long=>'num',     :short=>'n', :type=>'uint',   :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>'0'}
+casts << {:long=>'solexa',  :short=>'s', :type=>'flag',   :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
 
 PHRED_SCORES = Regexp.new('[!"#$%&\'()*+,-./0123456789:]')
 
@@ -52,7 +53,8 @@ if options.has_key? :data_in
   options[:data_in].each do |file|
     Fastq.open(file, mode='r') do |fastq|
       fastq.each do |entry|
-        entry.convert! if entry.qual.match PHRED_SCORES
+        entry.convert_phred2illumina!  if entry.qual.match PHRED_SCORES
+        entry.convert_solexa2illumina! if options[:solexa]
         bp.puts entry.to_bp
         num += 1
 
diff --git a/bp_test/out/read_fastq.out.3 b/bp_test/out/read_fastq.out.3
new file mode 100644
index 0000000..ae6f2a8
--- /dev/null
+++ b/bp_test/out/read_fastq.out.3
@@ -0,0 +1,5 @@
+SEQ_NAME: sanger
+SEQ: aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
+SEQ_LEN: 41
+SCORES: CCDDEFFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefgh
+---
diff --git a/bp_test/test/test_read_fastq b/bp_test/test/test_read_fastq
index 82b220c..0e3f3df 100755
--- a/bp_test/test/test_read_fastq
+++ b/bp_test/test/test_read_fastq
@@ -13,3 +13,7 @@ clean
 run "$bp -i $in -n 1 -O $tmp"
 assert_no_diff $tmp $out.2
 clean
+
+run "$bp -i $in -n 1 -s -O $tmp"
+assert_no_diff $tmp $out.3
+clean
diff --git a/code_ruby/Maasha/lib/seq.rb b/code_ruby/Maasha/lib/seq.rb
index b7cc44b..52f7e44 100644
--- a/code_ruby/Maasha/lib/seq.rb
+++ b/code_ruby/Maasha/lib/seq.rb
@@ -4,8 +4,8 @@ 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]
 
 # Quality scores bases
-SCORE_PHRED  = 33
-SCORE_SOLEXA = 64
+SCORE_PHRED    = 33
+SCORE_ILLUMINA = 64
 
 # Error class for all exceptions to do with Seq.
 class SeqError < StandardError; end
@@ -17,7 +17,7 @@ class Seq
   # - seq_name: Name of the sequence.
   # - seq: The sequence.
   # - type: The sequence type - DNA, RNA, or protein
-  # - qual: A Solexa type quality scores string.
+  # - qual: An Illumina type quality scores string.
   def initialize(seq_name = nil, seq = nil, type = nil, qual = nil)
     @seq_name = seq_name
     @seq      = seq
@@ -143,14 +143,38 @@ class Seq
 
   # Method to convert the quality scores from a specified base
   # to another base.
-  def convert!
+  def convert_phred2illumina!
     self.qual.gsub! /./ do |score|
       score_phred  = score.ord - SCORE_PHRED
       raise SeqError, "Bad Phred score: #{score} (#{score_phred})" unless (0 .. 40).include? score_phred
-      score_solexa = score_phred + SCORE_SOLEXA
-      score        = score_solexa.chr
+      score_illumina = score_phred + SCORE_ILLUMINA
+      score          = score_illumina.chr
     end
   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)
+    end
+  end
+
+  private
+
+  # 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
+  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
+  end
 end
 
 # Error class for all exceptions to do with Digest.
-- 
2.39.2