scbi_fastq 0.0.16 → 0.0.17

data/History.txt

@@ -1,3 +1,7 @@
+=== 0.0.17 2012-07-13
+
+Read gzip files
+
 === 0.0.16 2012-06-13
 
 Class method to_fastq saves with phred qualities

data/README.rdoc

@@ -13,10 +13,28 @@ scbi_fastq is a ruby gem to read/write FASTQ files (DNA/RNA sequences) with qual
 * Quality values can be automatically splitted
 * Write FASTQ files in Sanger format
 * Iteration over large files without extra memory usage
-
+* Can read gzip files directly
 
 == SYNOPSIS:
 
+=== Reading a compressed FASTQ in gzip with iterator:
+
+  require 'scbi_fastq'
+
+  # open gzip file in sanger mode
+  fqr=FastqFile.new('file1.fastq.gz')
+
+  fqr.each do |name,seq_fasta,qual,comments|
+
+    puts name
+    puts seq_fasta
+    puts qual
+    puts comments
+  end
+ 
+  fqr.close
+
+
 === Reading a FASTQ with iterator:
 
   require 'scbi_fastq'

data/lib/scbi_fastq.rb

@@ -3,5 +3,5 @@ $:.unshift(File.dirname(__FILE__)) unless
 
 require 'scbi_fastq/fastq_file'
 module ScbiFastq
-   VERSION = '0.0.16'
+   VERSION = '0.0.17'
 end

data/lib/scbi_fastq/fastq_file.rb

@@ -1,3 +1,4 @@
+require 'zlib'
 
 # add ord method to ruby 1.8
 if !String.instance_methods.include?(:ord)
@@ -30,7 +31,7 @@ class FastqFile
       end
 
       @fastq_file = File.open(fasta_file_name,'a')
-    else #read only
+    else #read only 
       if !File.exist?(fasta_file_name)
         raise "File #{fasta_file_name} doesn't exists"
       end
@@ -38,7 +39,14 @@ class FastqFile
       if fasta_file_name.is_a?(IO)
         @fastq_file = fasta_file_name
       else
-        @fastq_file = File.open(fasta_file_name,'r')
+        begin
+          @fastq_file = Zlib::GzipReader.open(fasta_file_name)
+          # puts "GZIP file detected"
+        rescue
+          @fastq_file = File.open(fasta_file_name,'r')
+          # puts "NORMAL file detected"
+        end
+        
       end
     end
 
@@ -127,10 +135,9 @@ class FastqFile
 
   # goto first position in file
   def rewind
-
     @num_seqs = 0 ;
-    @fastq_file.pos=0
-
+    # @fastq_file.pos=0
+    @fastq_file.rewind
   end
 
   #------------------------------------

data/test/test_scbi_fastq.rb

@@ -4,12 +4,33 @@ class TestScbiFastq < Test::Unit::TestCase
 
   def setup
    	@test_file='/tmp/sanger.fastq';
+   	
   	
   	@seq_fasta='ACTG'
 		@seq_qual=[31]
 	  @seq_name='SEQ'
 	  
   end
+
+  def test_gz_sanger
+    
+		fqr=FastqFile.new(File.join(File.dirname(__FILE__),'sanger2.fastq.gz'))
+
+		i=1
+		
+		fqr.each do |n,s,q|
+
+		  assert_equal(@seq_name+i.to_s,n)
+		  assert_equal(@seq_fasta*i,s)
+		  assert_equal((@seq_qual*i*@seq_fasta.length),q)
+
+			i+=1
+		end
+		 
+	  fqr.close			
+
+    
+  end
   
   
   def fill_file(n,offset=33)
@@ -134,7 +155,7 @@ class TestScbiFastq < Test::Unit::TestCase
 			i=1
 			
 			fqr.each do |n,s,q|
-        puts n,s,q
+        # puts n,s,q
         assert_equal(@seq_name+i.to_s,n)
         assert_equal(@seq_fasta*i,s)
         # assert_equal((@seq_qual*i*@seq_fasta.length),q)

metadata

@@ -2,7 +2,7 @@
 name: scbi_fastq
 version: !ruby/object:Gem::Version 
   prerelease: 
-  version: 0.0.16
+  version: 0.0.17
 platform: ruby
 authors: 
 - Dario Guerrero
@@ -10,7 +10,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2012-06-13 00:00:00 Z
+date: 2012-07-13 00:00:00 Z
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: hoe