X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=code_ruby%2Flib%2Fmaasha%2Fsff.rb;h=6b277e39b9c9b0e602c08ec386e56968e64df613;hb=fe96759f8f0cbc43b1b6965ee638c5415ef48c48;hp=0a9d2a1ffce40ccd0ba40f183b84a4e265cc2c74;hpb=494dc53ebd515b1e3e9b91bbebf43059899ca4ce;p=biopieces.git

diff --git a/code_ruby/lib/maasha/sff.rb b/code_ruby/lib/maasha/sff.rb
index 0a9d2a1..6b277e3 100644
--- a/code_ruby/lib/maasha/sff.rb
+++ b/code_ruby/lib/maasha/sff.rb
@@ -23,6 +23,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 require 'maasha/base36'
+require 'maasha/seq'
 
 # Error class for all exceptions to do with SFF.
 class SFFError < StandardError; end
@@ -35,8 +36,6 @@ BIT_MASK  = (1 << BIT_SHIFT) - 1
 class SFF
   include Enumerable
 
-  @@count = 0
-
   # Class method for opening SFF files.
   def self.open(*args)
     ios = File.open(*args)
@@ -69,6 +68,7 @@ class SFF
     @flow_chars               = ""
     @key_sequence             = ""
     @eight_byte_padding       = 0
+    @count                    = 0
 
     header_parse
   end
@@ -127,7 +127,7 @@ class SFF
 
   # Method to parse a read section of an SFF file.
   def read_parse
-    return nil if @number_of_reads == @@count
+    return nil if @number_of_reads == @count
 
     template = "nnNnnnn"
 
@@ -160,7 +160,7 @@ class SFF
 
     fast_forward
 
-    @@count += 1
+    @count += 1
 
     read
   end
@@ -195,7 +195,11 @@ class Read
 
   # Method that converts a Read object's data to a Biopiece record (a hash).
   def to_bp
-    coordinates_get
+    # Simulated SFF files may not have coordinates.
+    begin
+      coordinates_get
+    rescue
+    end
 
     hash = {}
 
@@ -206,13 +210,18 @@ class Read
     hash[:CLIP_QUAL_RIGHT]    = self.clip_qual_right    - 1
     hash[:CLIP_ADAPTOR_LEFT]  = self.clip_adapter_left  - 1
     hash[:CLIP_ADAPTOR_RIGHT] = self.clip_adaptor_right - 1
-    hash[:SCORES]             = self.quality_scores.map { |i| (i += 64).chr }.join ""
+    hash[:SCORES]             = self.quality_scores.map { |i| (i += Seq::SCORE_BASE).chr }.join ""
     hash[:X_POS]              = self.x_pos
     hash[:Y_POS]              = self.y_pos
 
     hash
   end
 
+  # Method that converts a Read object's data to a Seq object.
+  def to_seq
+    Seq.new(self.name, self.bases, nil, self.quality_scores.map { |i| (i += Seq::SCORE_BASE).chr }.join("") )
+  end
+
   # Method that soft masks the sequence (i.e. lowercases sequence) according to
   # clip_qual_left and clip_qual_right information.
   def mask
@@ -221,6 +230,8 @@ class Read
     right  = self.bases[self.clip_qual_right ... self.bases.length].downcase
 
     self.bases = left + middle + right
+
+    self
   end
 
   # Method that clips sequence (i.e. trims) according to
@@ -228,6 +239,8 @@ class Read
   def clip
     self.bases          = self.bases[self.clip_qual_left - 1 ... self.clip_qual_right]
     self.quality_scores = self.quality_scores[self.clip_qual_left - 1 ... self.clip_qual_right]
+
+    self
   end
 
   private