bio-ngs 0.3.2.alpha.01

data/test/helper.rb

@@ -0,0 +1,18 @@
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'test/unit'
+require 'shoulda'
+
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'bio-ngs'
+
+class Test::Unit::TestCase
+end

data/test/test_bio-ngs.rb

@@ -0,0 +1,17 @@
+require 'helper'
+
+class TestBioNgs < Test::Unit::TestCase
+  # should "probably rename this file and start testing for real" do
+  #   flunk "hey buddy, you should probably rename this file and start testing for real"
+  # end
+  
+  # def test_init
+  #   ngs = Ngs.new
+  #   assert_equal("", ngs.data)
+  # end
+  # 
+  # def test_bcl2fastq
+  #   z=Ngs.pippo
+  #   assert_equal("xxxx",z)
+  # end
+end

data/test/test_db.rb

@@ -0,0 +1,21 @@
+require 'helper'
+
+class TestHomology < Test::Unit::TestCase 
+
+  
+  context "Database class" do
+    
+    should "take the db type and an optional yaml file" do
+      db = Bio::Ngs::Db.new :ontology, "test/conf/test_db.yml"
+      assert_equal(Bio::Ngs::Db,db.class)
+    end
+    
+    should "raise an error if an invalid db type is called" do
+      assert_raise ArgumentError do
+        db = Bio::Ngs::Db.new :invalid_type
+      end
+    end
+    
+  end
+  
+end

data/test/test_homology.rb

@@ -0,0 +1,102 @@
+require 'helper'
+
+class TestHomology < Test::Unit::TestCase 
+  
+  def setup
+    db = Bio::Ngs::Db.new :homology, "test/conf/test_db.yml"
+    db.create_tables
+  end
+  
+  def teardown
+    FileUtils.rm "test/data/test.sqlite3" if File.exists? "test/data/test.sqlite3"
+  end
+  
+  context "Homology database" do
+    
+    should "have a set of empty tables created according to migrations" do
+      assert_equal(0,GoAnnotation.count)
+      assert_equal(0,BlastOutput.count)
+    end
+    
+    should "have a table blast_outputs" do
+      fields = BlastOutput.column_names
+      assert_equal(7,fields.size)
+      assert_equal(["id","query_id","target_id","target_description","evalue","identity","positive"],fields)
+    end
+    
+    should "have a table go_annotations" do
+      fields = GoAnnotation.column_names
+      assert_equal(16,fields.size)
+      assert_equal(["id","db","entry_id","symbol","qualifier","go_id","db_ref","evidence","additional_identifier","aspect","name","synonym","molecule_type","taxon_id","date","assigned_by"],fields)      
+    end
+    
+  end
+  
+  context "Homology import tasks" do
+    
+    should "take a GO Annotation file and store it into a go_annotations table" do
+      Bio::Ngs::Homology.goa_import("test/data/goa_uniprot","test/conf/test_db.yml")
+      goa = GoAnnotation.find(:first)
+      assert_equal("UniProtKB",goa.db)
+      assert_equal("Q5TM25",goa.entry_id)
+      assert_equal("AIF1",goa.symbol)
+      assert_equal("colocalizes_with",goa.qualifier)
+      assert_equal("GO:0032587",goa.go_id)
+      assert_equal("Allograft inflammatory factor 1",goa.name)
+      assert_equal("AIF1_MACMU|AIF1",goa.synonym)
+      assert_equal(27,GoAnnotation.count)
+      goa = GoAnnotation.find(:all)
+      assert_equal("Q5U241",goa[-1].entry_id)
+      assert_equal("GO:0008285",goa[-1].go_id)
+    end
+    
+    should "take a Blast XML file and store the results into a blast_outputs table" do
+      Bio::Ngs::Homology.blast_import("test/data/blastoutput.xml","test/conf/test_db.yml")
+      b = BlastOutput.find(:first)
+      assert_equal("ENSBTAG00000031386_1906_35",b.query_id)
+      assert_equal("Q5TTP0",b.target_id)
+      assert_equal("WD repeat-containing protein on Y chromosome OS=Anopheles gambiae GN=WDY PE=4 SV=4",b.target_description)
+      assert_equal(2.55108e-57,b.evalue)
+      assert_equal(29.50530035335689,b.identity)
+      assert_equal(47.879858657243815,b.positive)
+    end
+    
+  end
+  
+  context "Homology convert tasks" do
+    
+    should "create a tab-separated file starting from the Blast XML file" do
+      Bio::Ngs::Homology.blast2text("test/data/blastoutput.xml","test/data/blastoutput.txt")
+      f = File.read("test/data/blastoutput.txt")
+      header,record = f.split("\n")
+      assert_equal("Query ID\tTarget ID\tTarget Description\tE-value\tIdentity\tPositive",header)
+      elements = record.split("\t")
+      assert_equal("ENSBTAG00000031386_1906_35",elements[0])
+      assert_equal("sp|Q5TTP0|WDY_ANOGA",elements[1])
+      assert_equal("WD repeat-containing protein on Y chromosome OS=Anopheles gambiae GN=WDY PE=4 SV=4",elements[2])
+      assert_equal("2.55108e-57",elements[3])
+      assert_equal("29.50530035335689",elements[4])
+      assert_equal("47.879858657243815",elements[5])
+      FileUtils.rm "test/data/blastoutput.txt"
+    end
+    
+    should "create a JSON file with the GO Annotation present into the db" do
+      Bio::Ngs::Homology.goa_import("test/data/goa_uniprot","test/conf/test_db.yml")
+      Bio::Ngs::Homology.blast_import("test/data/blastoutput.xml","test/conf/test_db.yml")
+      Bio::Ngs::Homology.go_annotation_to_json("test/data/go_annotations.json","test","test/conf/test_db.yml")
+      data = JSON.parse File.read("test/data/go_annotations.json")
+      assert_equal(1,data.size)
+      data = data.first
+      assert_equal("ENSBTAG00000031386_1906_35",data["gene_id"])
+      assert_equal(3,data["go"].size)
+      assert_equal("GO:0003674",data["go"][0])
+      assert_equal("GO:0005575",data["go"][1])
+      assert_equal("GO:0008150",data["go"][2])
+      assert_equal("test",data["library"])
+      FileUtils.rm "test/data/go_annotations.json"
+    end
+    
+  end
+  
+  
+end

data/test/test_ngs.rb

@@ -0,0 +1,21 @@
+require 'helper'
+
+class TestNgs < Test::Unit::TestCase
+  # should "probably rename this file and start testing for real" do
+  #   flunk "hey buddy, you should probably rename this file and start testing for real"
+  # end
+
+  def setup
+    @qseq_str="HWI-BRUNOP16X   0001    8       1       15744   1220    0       1       GNAGCCGATCCACCTCCCAGCCTTCCTGGGATACAAGTCTGGCATGACTC      TBTTTTTTTT`^``Sdbd_deeeeeeeeeeeWUdd_bbbfdTedXOTTTS      1"
+  end
+  
+  def test_qseq2fastq_pe
+    #qseq_pe_output="@HWI-BRUNOP16X:8:1:15744:1220#0/1\nGNAGCCGATCCACCTCCCAGCCTTCCTGGGATACAAGTCTGGCATGACTC\n+\nTBTTTTTTTT`^``Sdbd_deeeeeeeeeeeWUdd_bbbfdTedXOTTTS"    
+    #assert_equal(qseq_pe_output, Bio::Ngs::Converter.qseq2fastq_pe(@qseq_str))
+  end
+
+  def test_qseq2fastq_se
+    #qseq_se_output="@HWI-BRUNOP16X:8:1:15744:1220#0/\nGNAGCCGATCCACCTCCCAGCCTTCCTGGGATACAAGTCTGGCATGACTC\n+\nTBTTTTTTTT`^``Sdbd_deeeeeeeeeeeWUdd_bbbfdTedXOTTTS"    
+    #assert_equal(qseq_se_output, Bio::Ngs::Converter.qseq2fastq_se(@qseq_str))
+  end
+end

data/test/test_ontology.rb

@@ -0,0 +1,74 @@
+require 'helper'
+
+class TestOntology < Test::Unit::TestCase 
+  
+  def setup
+    db = Bio::Ngs::Db.new :ontology, "test/conf/test_db.yml"
+    db.create_tables
+  end
+  
+  def teardown
+    FileUtils.rm "test/data/test.sqlite3" if File.exists? "test/data/test.sqlite3"
+  end
+  
+  context "Ontology database" do
+    
+    should "have a set of empty tables created according to migrations" do
+      assert_equal(0,Gene.count)
+      assert_equal(0,Go.count)
+      assert_equal(0,GeneGo.count)
+    end
+    
+    should "have a table go" do
+      fields = Go.column_names
+      assert_equal(5,fields.size)
+      assert_equal(["id","go_id","name","namespace","is_a"],fields)
+    end
+    
+  end
+  
+  context "Ontology import tasks" do
+    
+    should "take a GO OBO file and store it into go table" do
+      Bio::Ngs::Ontology.go_import("test/data/goslim_goa.obo","test/conf/test_db.yml")
+      r = Go.find(:first)
+      assert_equal("GO:0000003",r.go_id)
+      assert_equal("reproduction",r.name)
+      assert_equal("biological_process",r.namespace)
+      assert_equal("GO:0008150 ",r.is_a)
+      go = Go.find(:all)
+      assert_equal("GO:0071941",go[-1].go_id)
+      assert_equal("nitrogen cycle metabolic process",go[-1].name)
+      assert_equal("biological_process",go[-1].namespace)
+      total = Go.count
+      assert_equal(106,total)
+    end
+    
+  end
+  
+  
+  context "Bio::Ngs::Ontology" do
+    
+    should "store into the db the GO terms associated to Genes" do
+      Bio::Ngs::Ontology.go_import("test/data/goslim_goa.obo","test/conf/test_db.yml")
+      Bio::Ngs::Ontology.load_go_genes("test/data/gene-GO.json","test/conf/test_db.yml")
+
+      db = Bio::Ngs::Db.new :ontology, "test/conf/test_db.yml"
+      assert_equal(2,Gene.count)
+      assert_equal(14,GeneGo.count)
+      ontology = %w(GO:0005622 GO:0005634 GO:0005654 GO:0005737 GO:0007049 GO:0007059 GO:0043234)
+      terms = Gene.find(1).go.map {|g| g.go_id}
+      assert_equal(ontology,terms.sort)
+      ontology = %w(GO:0005634 GO:0005654 GO:0005737 GO:0007049 GO:0008283 GO:0043234 GO:0051276)
+      terms = Gene.find(2).go.map {|g| g.go_id}
+      assert_equal(ontology,terms.sort)
+      
+      assert_equal("BRCA1",Gene.find(1).library)
+      assert_equal("BRCA2",Gene.find(2).library)
+      
+    end
+    
+  end
+  
+  
+end

data/test/test_utils.rb

@@ -0,0 +1,29 @@
+require "#{File.dirname(__FILE__)}/helper"
+
+class TestUtils < Test::Unit::TestCase
+  
+  def test_plugin_binary
+    assert_nothing_raised do
+      Bio::Ngs::Utils.binary("sff_extract")
+    end
+  end
+  
+  def test_plugin_os_binary
+    assert_nothing_raised do
+      Bio::Ngs::Utils.binary("samtools")
+    end
+  end
+  
+  def test_os_binary
+    assert_nothing_raised do
+      Bio::Ngs::Utils.binary("ruby")
+    end
+  end
+  
+  def test_raise_error
+    assert_raise Bio::Ngs::Utils::BinaryNotFound do
+      Bio::Ngs::Utils.binary("fake_binary")
+    end
+  end
+  
+end

metadata

@@ -0,0 +1,460 @@
+--- !ruby/object:Gem::Specification
+name: bio-ngs
+version: !ruby/object:Gem::Version
+  version: 0.3.2.alpha.01
+  prerelease: 6
+platform: ruby
+authors:
+- Francesco Strozzi
+- Raoul J.P. Bonnal
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2011-10-10 00:00:00.000000000Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: &2170881740 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+  type: :runtime
+  prerelease: false
+  version_requirements: *2170881740
+- !ruby/object:Gem::Dependency
+  name: bio-bwa
+  requirement: &2170874980 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.2.2
+  type: :runtime
+  prerelease: false
+  version_requirements: *2170874980
+- !ruby/object:Gem::Dependency
+  name: bio-samtools
+  requirement: &2170868580 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.0.0
+  type: :runtime
+  prerelease: false
+  version_requirements: *2170868580
+- !ruby/object:Gem::Dependency
+  name: thor
+  requirement: &2170865400 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.14.6
+  type: :runtime
+  prerelease: false
+  version_requirements: *2170865400
+- !ruby/object:Gem::Dependency
+  name: rubyvis
+  requirement: &2170863100 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.5.0
+  type: :runtime
+  prerelease: false
+  version_requirements: *2170863100
+- !ruby/object:Gem::Dependency
+  name: daemons
+  requirement: &2170860560 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.1.0
+  type: :runtime
+  prerelease: false
+  version_requirements: *2170860560
+- !ruby/object:Gem::Dependency
+  name: ruby-ensembl-api
+  requirement: &2170857700 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.0.1
+  type: :runtime
+  prerelease: false
+  version_requirements: *2170857700
+- !ruby/object:Gem::Dependency
+  name: activerecord
+  requirement: &2170855960 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 3.0.5
+  type: :runtime
+  prerelease: false
+  version_requirements: *2170855960
+- !ruby/object:Gem::Dependency
+  name: sqlite3
+  requirement: &2170854340 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.3.3
+  type: :runtime
+  prerelease: false
+  version_requirements: *2170854340
+- !ruby/object:Gem::Dependency
+  name: bio-blastxmlparser
+  requirement: &2170851720 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: *2170851720
+- !ruby/object:Gem::Dependency
+  name: progressbar
+  requirement: &2170848640 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.9.0
+  type: :runtime
+  prerelease: false
+  version_requirements: *2170848640
+- !ruby/object:Gem::Dependency
+  name: shoulda
+  requirement: &2170844080 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: *2170844080
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: &2170840920 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.0.0
+  type: :development
+  prerelease: false
+  version_requirements: *2170840920
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: &2170839560 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.5.2
+  type: :development
+  prerelease: false
+  version_requirements: *2170839560
+- !ruby/object:Gem::Dependency
+  name: rcov
+  requirement: &2170838040 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: *2170838040
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: &2170836560 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+  type: :development
+  prerelease: false
+  version_requirements: *2170836560
+- !ruby/object:Gem::Dependency
+  name: thor
+  requirement: &2170834960 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.14.6
+  type: :development
+  prerelease: false
+  version_requirements: *2170834960
+- !ruby/object:Gem::Dependency
+  name: ffi
+  requirement: &2170831480 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.0.6
+  type: :development
+  prerelease: false
+  version_requirements: *2170831480
+- !ruby/object:Gem::Dependency
+  name: rubyvis
+  requirement: &2170828140 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.5.0
+  type: :development
+  prerelease: false
+  version_requirements: *2170828140
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: &2170826120 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 2.5.0
+  type: :development
+  prerelease: false
+  version_requirements: *2170826120
+- !ruby/object:Gem::Dependency
+  name: daemons
+  requirement: &2170824340 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.1.0
+  type: :development
+  prerelease: false
+  version_requirements: *2170824340
+- !ruby/object:Gem::Dependency
+  name: bio-samtools
+  requirement: &2170822080 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.0.0
+  type: :development
+  prerelease: false
+  version_requirements: *2170822080
+- !ruby/object:Gem::Dependency
+  name: ruby-ensembl-api
+  requirement: &2170819520 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.0.1
+  type: :development
+  prerelease: false
+  version_requirements: *2170819520
+- !ruby/object:Gem::Dependency
+  name: bio-bwa
+  requirement: &2170816740 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.2.2
+  type: :development
+  prerelease: false
+  version_requirements: *2170816740
+- !ruby/object:Gem::Dependency
+  name: activerecord
+  requirement: &2170814180 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 3.0.5
+  type: :development
+  prerelease: false
+  version_requirements: *2170814180
+- !ruby/object:Gem::Dependency
+  name: sqlite3
+  requirement: &2170805160 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.3.3
+  type: :development
+  prerelease: false
+  version_requirements: *2170805160
+- !ruby/object:Gem::Dependency
+  name: bio-blastxmlparser
+  requirement: &2170803260 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: *2170803260
+- !ruby/object:Gem::Dependency
+  name: progressbar
+  requirement: &2170801680 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.9.0
+  type: :development
+  prerelease: false
+  version_requirements: *2170801680
+- !ruby/object:Gem::Dependency
+  name: json
+  requirement: &2170800800 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: *2170800800
+description: bio-ngs provides a framework for handling NGS data with BioRuby
+email: francesco.strozzi@gmail.com
+executables:
+- biongs
+extensions:
+- ext/mkrf_conf.rb
+extra_rdoc_files:
+- LICENSE.txt
+- README.rdoc
+files:
+- .document
+- Gemfile
+- Gemfile.lock
+- LICENSE.txt
+- README.rdoc
+- Rakefile
+- VERSION
+- bin/biongs
+- bio-ngs.gemspec
+- ext/mkrf_conf.rb
+- lib/bio-ngs.rb
+- lib/bio/appl/ngs/bcl2qseq.rb
+- lib/bio/appl/ngs/blast.rb
+- lib/bio/appl/ngs/bowtie-inspect.rb
+- lib/bio/appl/ngs/cufflinks.rb
+- lib/bio/appl/ngs/fastx.rb
+- lib/bio/appl/ngs/samtools.rb
+- lib/bio/appl/ngs/sff_extract.rb
+- lib/bio/appl/ngs/tophat.rb
+- lib/bio/ngs/converter.rb
+- lib/bio/ngs/core_ext.rb
+- lib/bio/ngs/db.rb
+- lib/bio/ngs/db/migrate/homology/201105030707_create_blastout.rb
+- lib/bio/ngs/db/migrate/homology/201105030709_create_goannotation.rb
+- lib/bio/ngs/db/migrate/ontology/201105030708_create_go.rb
+- lib/bio/ngs/db/migrate/ontology/201105030710_create_gene_go.rb
+- lib/bio/ngs/db/migrate/ontology/201105030711_create_gene.rb
+- lib/bio/ngs/db/models.rb
+- lib/bio/ngs/db/models/homology.rb
+- lib/bio/ngs/db/models/ontology.rb
+- lib/bio/ngs/ext/bin/common/fastq_coverage_graph.sh
+- lib/bio/ngs/ext/bin/common/sff_extract
+- lib/bio/ngs/ext/bin/linux/samtools
+- lib/bio/ngs/ext/bin/osx/samtools
+- lib/bio/ngs/ext/versions.yaml
+- lib/bio/ngs/graphics.rb
+- lib/bio/ngs/homology.rb
+- lib/bio/ngs/ontology.rb
+- lib/bio/ngs/quality.rb
+- lib/bio/ngs/record.rb
+- lib/bio/ngs/task.rb
+- lib/bio/ngs/utils.rb
+- lib/development_tasks.rb
+- lib/enumerable.rb
+- lib/tasks/bwa.thor
+- lib/tasks/convert.thor
+- lib/tasks/history.thor
+- lib/tasks/homology.thor
+- lib/tasks/ontology.thor
+- lib/tasks/project.thor
+- lib/tasks/quality.thor
+- lib/tasks/rna.thor
+- lib/tasks/sff_extract.thor
+- lib/templates/README.tt
+- lib/templates/db.tt
+- lib/wrapper.rb
+- spec/converter_qseq_spec.rb
+- spec/fixture/s_1_1_1108_qseq.txt
+- spec/quality_spec.rb
+- spec/sff_extract_spec.rb
+- spec/spec_helper.rb
+- spec/tophat_spec.rb
+- spec/utils_spec.rb
+- test/conf/test_db.yml
+- test/data/blastoutput.xml
+- test/data/gene-GO.json
+- test/data/goa_uniprot
+- test/data/goslim_goa.obo
+- test/helper.rb
+- test/test_bio-ngs.rb
+- test/test_db.rb
+- test/test_homology.rb
+- test/test_ngs.rb
+- test/test_ontology.rb
+- test/test_utils.rb
+homepage: http://github.com/helios/bioruby-ngs
+licenses:
+- MIT
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+      segments:
+      - 0
+      hash: 1963233679841043858
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>'
+    - !ruby/object:Gem::Version
+      version: 1.3.1
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.6
+signing_key: 
+specification_version: 3
+summary: bio-ngs provides a framework for handling NGS data with BioRuby
+test_files:
+- spec/converter_qseq_spec.rb
+- spec/quality_spec.rb
+- spec/sff_extract_spec.rb
+- spec/spec_helper.rb
+- spec/tophat_spec.rb
+- spec/utils_spec.rb
+- test/helper.rb
+- test/test_bio-ngs.rb
+- test/test_db.rb
+- test/test_homology.rb
+- test/test_ngs.rb
+- test/test_ontology.rb
+- test/test_utils.rb