bio-gngm 0.1.0

data/test/data/test_chr.fasta.amb

@@ -0,0 +1,2 @@
+69930 1 1
+41554 50 N

data/test/data/test_chr.fasta.ann

@@ -0,0 +1,3 @@
+69930 1 11
+0 chr_1 (null)
+0 69930 1

data/test/data/test_chr.fasta.fai

@@ -0,0 +1 @@
+chr_1	69930	7	70	71

data/test/helper.rb

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+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-gngm'
+
+class Test::Unit::TestCase
+end

data/test/test_bio-gngm.rb

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+require 'helper'
+
+class TestBioGngm < Test::Unit::TestCase
+  
+  context "Classes in bio/db/sam" do
+    should "contain Pileup" do
+      assert_instance_of Bio::DB::Pileup, Bio::DB::Pileup.new("seq1\t272\tT\t24\t,.$.....,,.,.,...,,,.,..^+.\t<<<+;<<<<<<<<<<<=<;<;7<&")
+    end
+  
+    should "contain Vcf " do
+      assert_instance_of Bio::DB::Vcf, Bio::DB::Vcf.new("20	14370	rs6054257	G	A	29	0	NS=3;DP=14;AF=0.5;DB;H2	GT:GQ:DP:HQ	0|0:48:1:51,51	1|0:48:8:51,51	1/1:43:5:-1,-1")
+    end
+  end
+  
+  context "A Pileup instance" do
+    setup do
+      @p1 = Bio::DB::Pileup.new("seq1\t272\tT\t10\t,.$.....,,.^+.\t<<<+;<<<<<<<<<<<=<;<;7<&")
+      @p2 = Bio::DB::Pileup.new("seq1\t272\tT\t24\taaaaaaaaaaaa............\t<<<+;<<<<<<<<<<<=<;<;7<&")
+      @p3 = Bio::DB::Pileup.new("seq1\t272\tT\t24\taaaaaaaaaaaaaaaaaaaaaaaa\t<<<+;<<<<<<<<<<<=<;<;7<&")
+      @p4 = Bio::DB::Pileup.new("seq1\t272\tT\t9\taaaaaaaGGC\t<<<+;<<<<<<<<<<<=<;<;7<&")
+    end
+    
+    should "calculate discordant chastity" do
+      assert_equal @p1.discordant_chastity, 0.0
+      assert_equal @p2.discordant_chastity, 0.5
+      assert_equal @p3.discordant_chastity, 1.0
+      assert_equal @p4.discordant_chastity, 0.7777777777777778
+    end
+    
+    should "know it is a snp" do
+      assert @p2.is_snp?(:min_depth => 5, :min_non_ref => 5)
+      assert !@p1.is_snp?(:min_depth => 5, :min_non_ref => 5)
+    end
+  end
+  
+  context "A Gngm object" do
+    setup do
+      @g1 = Bio::Util::Gngm.new(:file => "test/data/testu.bam", 
+                     :format => :bam, 
+                     :fasta => "test/data/test_chr.fasta", 
+                     :samtools => {:r => "chr_1:100-300"}
+                     )
+      @g1.snp_positions
+      
+      @g2 = Bio::Util::Gngm.new(:file => "/Users/macleand/Desktop/ngm/fli.sorted.bam", 
+                     :format => :bam, 
+                     :fasta => "/Users/macleand/Desktop/ngm/TAIR9_chr_all.fas", 
+                     :samtools => {:r => "1:100-10000"},
+                     :histo_bin_width => 100,
+
+      )
+    end
+    
+    
+    should "open BAM files" do
+      assert_instance_of Bio::DB::Sam, @g1.file
+    end
+    
+    should "return array of snps annotated with discordant chastity" do
+      assert_instance_of Array, @g1.snp_positions
+      assert_equal [[185, 0.3333333333333333], [203, 0.3333333333333333], [279, 0.5]], @g1.snp_positions
+    end
+    
+    should "draw a picture of a SNP histogram" do
+      @g1.frequency_histogram("test_histo.png")
+      assert File.exists?("test_histo.png")
+      File.delete("test_histo.png")
+    end
+    
+    should "get chastity threads" do
+      @g1.snp_positions
+      assert_equal [[0.3, [185, 203]],[0.4, []],[0.5, [279]], [0.6000000000000001, []], [0.7, []],[0.8, []],[0.9000000000000001, []],[1.0, []]], @g1.threads(:start => 0.3, :stop => 1, :slide => 0.1, :size => 0.1)
+    end
+    
+    should "draw chastity threads" do
+      @g2.snp_positions
+      @g2.calculate_clusters(:k =>4, :set_seed => 1)
+      @g2.draw_threads("test_threads.png")
+      assert File.exists?("test_threads.png")
+      #File.delete("test_threads.png")
+    end
+
+
+    should "return lists of densities for each window from R" do
+      @g1.snp_positions
+      #puts @g1.densities[0]
+      assert_instance_of Array, @g1.densities
+      assert_instance_of Array, @g1.densities.first
+      assert_equal 0.24, @g1.densities[0].first
+    end
+    
+    should "find index of window in the @densities array" do
+      @g2.snp_positions
+      assert_equal 65, @g2.find_index(1.0)
+    end
+    
+    should "find bands ie cluster and return list of threads in that cluster together" do
+      @g2.snp_positions
+      @g2.calculate_clusters(:k => 4, :set_seed => 1)  ##due to randomness of clustering, its currently hard to make sure this is exactly tested.. 
+                                                        #setting the seed ensures consistent clustering ...
+      assert_equal [0.21000000000000002, 0.22, 0.8200000000000001, 0.8300000000000001, 0.8400000000000001, 0.8500000000000001, 0.8600000000000001, 0.97, 0.98, 0.99, 1.0], @g2.get_band(0.22)  
+    end
+    
+    should "draw found bands" do
+      @g2.snp_positions
+      @g2.calculate_clusters(:k => 4, :set_seed => 1)
+      @g2.draw_bands("test_bands.png")
+      assert File.exists?("test_bands.png")
+      #File.delete("test_bands.png")
+    end
+    
+    should "draw_signal_plots" do
+      @g2.snp_positions
+      @g2.calculate_clusters(:k => 4, :set_seed => 1)
+      @g2.draw_signal("signal.png")
+      File.delete("signal.png")
+    end
+    
+    should "calculate signal" do
+      @g2.snp_positions
+      @g2.calculate_clusters(:k => 4, :set_seed => 1)
+      assert_equal 1.157971267690456, @g2.signal.last
+    end
+  end
+  
+end

metadata

@@ -0,0 +1,276 @@
+--- !ruby/object:Gem::Specification
+name: bio-gngm
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+  prerelease: 
+platform: ruby
+authors:
+- Dan MacLean
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2012-03-19 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: &70226478302620 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+  type: :runtime
+  prerelease: false
+  version_requirements: *70226478302620
+- !ruby/object:Gem::Dependency
+  name: bio-samtools
+  requirement: &70226478299960 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.5.0
+  type: :runtime
+  prerelease: false
+  version_requirements: *70226478299960
+- !ruby/object:Gem::Dependency
+  name: rinruby
+  requirement: &70226478297240 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 2.0.2
+  type: :runtime
+  prerelease: false
+  version_requirements: *70226478297240
+- !ruby/object:Gem::Dependency
+  name: shoulda
+  requirement: &70226478383720 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: *70226478383720
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: &70226478382700 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.0.0
+  type: :development
+  prerelease: false
+  version_requirements: *70226478382700
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: &70226478381080 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: *70226478381080
+- !ruby/object:Gem::Dependency
+  name: rcov
+  requirement: &70226478380320 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: *70226478380320
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: &70226478379680 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+  type: :development
+  prerelease: false
+  version_requirements: *70226478379680
+- !ruby/object:Gem::Dependency
+  name: bio-samtools
+  requirement: &70226478379180 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.5.0
+  type: :development
+  prerelease: false
+  version_requirements: *70226478379180
+- !ruby/object:Gem::Dependency
+  name: rinruby
+  requirement: &70226478378620 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 2.0.2
+  type: :development
+  prerelease: false
+  version_requirements: *70226478378620
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: &70226478378060 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: *70226478378060
+description: Identify causative mutations in a model genome from NGS reads using the
+  NGM method.
+email: maclean.daniel@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files:
+- LICENSE.txt
+- README.rdoc
+files:
+- .document
+- Gemfile
+- Gemfile.lock
+- LICENSE.txt
+- README.rdoc
+- Rakefile
+- VERSION
+- bio-gngm.gemspec
+- doc/Bio.html
+- doc/Bio/DB.html
+- doc/Bio/DB/Pileup.html
+- doc/Bio/DB/Vcf.html
+- doc/Bio/Util.html
+- doc/Bio/Util/Gngm.html
+- doc/LICENSE_txt.html
+- doc/_index.html
+- doc/class_list.html
+- doc/created.rid
+- doc/css/common.css
+- doc/css/full_list.css
+- doc/css/style.css
+- doc/doc/created.rid
+- doc/file_list.html
+- doc/frames.html
+- doc/images/add.png
+- doc/images/bands.png
+- doc/images/brick.png
+- doc/images/brick_link.png
+- doc/images/bug.png
+- doc/images/bullet_black.png
+- doc/images/bullet_toggle_minus.png
+- doc/images/bullet_toggle_plus.png
+- doc/images/date.png
+- doc/images/delete.png
+- doc/images/find.png
+- doc/images/loadingAnimation.gif
+- doc/images/macFFBgHack.png
+- doc/images/package.png
+- doc/images/page_green.png
+- doc/images/page_white_text.png
+- doc/images/page_white_width.png
+- doc/images/plugin.png
+- doc/images/ruby.png
+- doc/images/signal.png
+- doc/images/tag_blue.png
+- doc/images/tag_green.png
+- doc/images/threads.png
+- doc/images/transparent.png
+- doc/images/wrench.png
+- doc/images/wrench_orange.png
+- doc/images/zoom.png
+- doc/index.html
+- doc/js/app.js
+- doc/js/darkfish.js
+- doc/js/full_list.js
+- doc/js/jquery.js
+- doc/js/navigation.js
+- doc/js/search.js
+- doc/js/search_index.js
+- doc/js/searcher.js
+- doc/lib/bio-gngm_rb.html
+- doc/lib/bio/util/bio-gngm_rb.html
+- doc/method_list.html
+- doc/rdoc.css
+- doc/table_of_contents.html
+- examples/.DS_Store
+- examples/make_histograms.rb
+- examples/make_threads.rb
+- examples/make_threads_isize.rb
+- examples/use_indels.rb
+- lib/bio-gngm.rb
+- lib/bio/util/bio-gngm.rb
+- scripts/get_subseq.rb
+- scripts/make_histograms_laerfyve.rb
+- scripts/make_histograms_laerfyve_stitched.rb
+- scripts/make_threads_isize_laerfyfe.rb
+- scripts/make_threads_unmapped_laerfyfe.rb
+- scripts/make_threads_unmapped_laerfyfe_pseudo.rb
+- scripts/make_threads_unmapped_simulation.rb
+- scripts/make_threads_unmapped_simulation_immediate_region.rb
+- scripts/optimise_freq_window_size.rb
+- stitched_contigs.zip
+- test/data/ids2.txt
+- test/data/sorted.bam
+- test/data/test
+- test/data/test.bam
+- test/data/test.fa
+- test/data/test.fai
+- test/data/test.sai
+- test/data/test.tam
+- test/data/test_chr.fasta
+- test/data/test_chr.fasta.amb
+- test/data/test_chr.fasta.ann
+- test/data/test_chr.fasta.bwt
+- test/data/test_chr.fasta.fai
+- test/data/test_chr.fasta.pac
+- test/data/test_chr.fasta.rbwt
+- test/data/test_chr.fasta.rpac
+- test/data/test_chr.fasta.rsa
+- test/data/test_chr.fasta.sa
+- test/data/testu.bam
+- test/data/testu.bam.bai
+- test/helper.rb
+- test/test_bio-gngm.rb
+homepage: http://github.com/danmaclean/bioruby-gngm
+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: 3948590901607660961
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.10
+signing_key: 
+specification_version: 3
+summary: Next-Generation Mapping of Mutations
+test_files: []