scbi_fastq 0.0.17 → 0.0.18

checksums.yaml

@@ -0,0 +1,15 @@
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+!binary "U0hBMQ==":
+  metadata.gz: !binary |-
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+SHA512:
+  metadata.gz: !binary |-
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data/History.txt

@@ -1,3 +1,7 @@
+=== 0.0.18 2013-12-16
+
+Write GZ
+
 === 0.0.17 2012-07-13
 
 Read gzip files

data/lib/scbi_fastq.rb

@@ -3,5 +3,5 @@ $:.unshift(File.dirname(__FILE__)) unless
 
 require 'scbi_fastq/fastq_file'
 module ScbiFastq
-   VERSION = '0.0.17'
+   VERSION = '0.0.18'
 end

data/lib/scbi_fastq/fastq_file.rb

@@ -23,7 +23,10 @@ class FastqFile
   def initialize(fasta_file_name, mode='r', fastq_type = :sanger, qual_to_array=true, qual_to_phred=true)
 
 
-    if mode.upcase.index('W')
+     
+    if mode.upcase.index('W.GZ')
+      @fastq_file = Zlib::GzipWriter.open(fasta_file_name)
+    elsif mode.upcase.index('W')
       @fastq_file = File.open(fasta_file_name,'w')
     elsif mode.upcase.index('A')
       if !File.exist?(fasta_file_name)

data/test/test_scbi_fastq.rb

@@ -4,6 +4,7 @@ class TestScbiFastq < Test::Unit::TestCase
 
   def setup
    	@test_file='/tmp/sanger.fastq';
+    @test_file_gz='/tmp/sanger.fastq.gz';
    	
   	
   	@seq_fasta='ACTG'
@@ -167,6 +168,44 @@ class TestScbiFastq < Test::Unit::TestCase
   end
   
 
+  def fill_file_gz(n,offset=33)
+    f=FastqFile.new(@test_file_gz,'w.gz')
+    puts "FILE GZ"
+    n.times do |c|
+      i = c+1
+      
+      name = "#{@seq_name+i.to_s}"
+      f.write_seq(name,@seq_fasta*i,(@seq_qual*i*@seq_fasta.length),'comments')
+      # f.puts('@'+name)
+      # f.puts(@seq_fasta*i)
+      # f.puts('+'+name)
+      # f.puts((@seq_qual*i*@seq_fasta.length).map{|e| (e+offset).chr}.join)
+    end
+    
+    f.close
+  end
+
+  def test_each_gz
+           # make new file and fill with data
+      fill_file_gz(100)  
+    
+
+      fqr=FastqFile.new(@test_file_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
+      assert_equal(i,101)
+
+      fqr.close 
+  end
 
   
   # def test_open_file

metadata

@@ -1,40 +1,69 @@
---- !ruby/object:Gem::Specification 
+--- !ruby/object:Gem::Specification
 name: scbi_fastq
-version: !ruby/object:Gem::Version 
-  prerelease: 
-  version: 0.0.17
+version: !ruby/object:Gem::Version
+  version: 0.0.18
 platform: ruby
-authors: 
+authors:
 - Dario Guerrero
 autorequire: 
 bindir: bin
 cert_chain: []
-
-date: 2012-07-13 00:00:00 Z
-dependencies: 
-- !ruby/object:Gem::Dependency 
-  name: hoe
+date: 2013-12-16 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '4.0'
+  type: :development
   prerelease: false
-  requirement: &id001 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        version: 2.8.0
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '4.0'
+- !ruby/object:Gem::Dependency
+  name: newgem
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.5.3
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.5.3
+- !ruby/object:Gem::Dependency
+  name: hoe
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.7'
   type: :development
-  version_requirements: *id001
-description: scbi_fastq is a ruby gem to read/write FASTQ files (DNA/RNA sequences) with qualities in a variety of formats (Sanger, Solexa, Ilumina).
-email: 
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.7'
+description: scbi_fastq is a ruby gem to read/write FASTQ files (DNA/RNA sequences)
+  with qualities in a variety of formats (Sanger, Solexa, Ilumina).
+email:
 - dariogf@scbi.uma.es
 executables: []
-
 extensions: []
-
-extra_rdoc_files: 
+extra_rdoc_files:
 - History.txt
 - Manifest.txt
 - PostInstall.txt
-files: 
+- README.rdoc
+files:
 - History.txt
 - Manifest.txt
 - PostInstall.txt
@@ -47,34 +76,34 @@ files:
 - script/generate
 - test/test_helper.rb
 - test/test_scbi_fastq.rb
+- .gemtest
 homepage: http://www.scbi.uma.es/downloads
-licenses: []
-
+licenses:
+- MIT
+metadata: {}
 post_install_message: PostInstall.txt
-rdoc_options: 
+rdoc_options:
 - --main
 - README.rdoc
-require_paths: 
+require_paths:
 - lib
-required_ruby_version: !ruby/object:Gem::Requirement 
-  none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      version: "0"
-required_rubygems_version: !ruby/object:Gem::Requirement 
-  none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      version: "0"
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
 requirements: []
-
 rubyforge_project: scbi_fastq
-rubygems_version: 1.8.24
+rubygems_version: 2.1.11
 signing_key: 
-specification_version: 3
-summary: scbi_fastq is a ruby gem to read/write FASTQ files (DNA/RNA sequences) with qualities in a variety of formats (Sanger, Solexa, Ilumina).
-test_files: 
-- test/test_helper.rb
+specification_version: 4
+summary: scbi_fastq is a ruby gem to read/write FASTQ files (DNA/RNA sequences) with
+  qualities in a variety of formats (Sanger, Solexa, Ilumina).
+test_files:
 - test/test_scbi_fastq.rb
+- test/test_helper.rb