finished refactoring s/has_key?/[]/

[biopieces.git] / code_ruby / lib / maasha / fastq.rb

diff --git a/code_ruby/lib/maasha/fastq.rb b/code_ruby/lib/maasha/fastq.rb
index b3ba85fba466bb2048a020365c8d06093ea13276..4ac44aa70cb84045158fc775f782be7719fdbbbd 100644 (file)
--- a/code_ruby/lib/maasha/fastq.rb
+++ b/code_ruby/lib/maasha/fastq.rb
@@ -28,33 +28,83 @@ require 'maasha/filesys'
 # Error class for all exceptions to do with FASTQ.
 class FastqError < StandardError; end
 
+# Class for parsing FASTQ entries from an ios and return as Seq objects.
 class Fastq < Filesys
-  # Method to get the next FASTQ entry form an ios and return this
+  # Method to get the next FASTQ entry from an ios and return this
   # as a Seq object. If no entry is found or eof then nil is returned.
   def get_entry
     begin
       seq_name       = @io.gets.chomp!
       seq            = @io.gets.chomp!
-      qual_name      = @io.gets.chomp!
+      @io.gets
       qual           = @io.gets.chomp!
 
       entry          = Seq.new
-      entry.type     = @type.nil? ? nil : @type.downcase
       entry.seq      = seq
       entry.seq_name = seq_name[1 .. seq_name.length]
       entry.qual     = qual
+      entry.type     = nil
 
       entry
     rescue
       nil
     end
   end
+end
+
+# Class for indesing FASTQ entries. The index will be
+# a hash with the FASTQ sequence name as key and a 
+# FastqElem as value. The latter contains info on
+# byte offset and length for each entry.
+class FastqIndex
+  HEADCHAR = 1
+  NEWLINE  = 1
+
+  attr_accessor :ios
+
+  # Method to initialize a FastqIndex object. For reading
+  # entries from file an _ios_ object must be supplied.
+  def initialize(ios = nil)
+    @ios    = ios
+    @index  = {}
+    @offset = 0
+  end
+
+  # Method to add a Fastq entry to a FastqIndex.
+  def add(entry)
+    offset_seq  = @offset + HEADCHAR + entry.seq_name.length + NEWLINE
+    offset_qual = @offset + HEADCHAR + entry.seq_name.length + NEWLINE + entry.length + NEWLINE + HEADCHAR + NEWLINE
+
+    @index[entry.seq_name] = FastqElem.new(offset_seq, offset_qual, entry.length)
+    
+    @offset += HEADCHAR + entry.seq_name.length + NEWLINE + entry.length + NEWLINE + HEADCHAR + NEWLINE + entry.length + NEWLINE
+  end
+
+  # Method to read from file a Fastq entry from an indexed position,
+  # and return the entry as a Seq object.
+  def get(seq_name)
+    raise FastqError, "Sequence name: #{seq_name} not found in index." unless @index[seq_name]
+
+    elem = @index[seq_name]
+    @ios.sysseek(elem.offset_seq)
+    seq = @ios.sysread(elem.length)
+    @ios.sysseek(elem.offset_qual)
+    qual = @ios.sysread(elem.length)
+
+    Seq.new(seq_name, seq, nil, qual)
+  end
+
+  private
+
+  # Class for storing index information to be used
+  # with disk based index.
+  class FastqElem
+    attr_reader :offset_seq, :offset_qual, :length
 
-  # TODO - this should be some custom to_s method instead.
-  def puts(record)
-    if record.has_key? :SEQ_NAME and record.has_key? :SEQ
-      @io.print ">#{record[:SEQ_NAME]}\n"
-      @io.print "#{record[:SEQ]}\n"
+    def initialize(offset_seq, offset_qual, length)
+      @offset_seq  = offset_seq
+      @offset_qual = offset_qual
+      @length      = length
     end
   end
 end