transfuse 0.1.1

data/test/data/contig_scores1.csv

@@ -0,0 +1,100 @@
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data/test/helper.rb

@@ -0,0 +1,16 @@
+require 'simplecov'
+require 'coveralls'
+
+SimpleCov.formatter = SimpleCov::Formatter::MultiFormatter[
+  SimpleCov::Formatter::HTMLFormatter,
+  Coveralls::SimpleCov::Formatter
+]
+SimpleCov.start
+
+require 'test/unit'
+begin; require 'turn/autorun'; rescue LoadError; end
+require 'shoulda-context'
+require 'transfuse'
+
+Turn.config.format = :pretty
+Turn.config.trace = 5

data/test/test_cluster.rb

@@ -0,0 +1,36 @@
+#!/usr/bin/env  ruby
+
+require 'helper'
+require 'tmpdir'
+
+class TestCluster < Test::Unit::TestCase
+
+  context 'cluster' do
+
+    setup do
+      @cluster = Transfuse::Cluster.new 4
+    end
+
+    teardown do
+    end
+
+    should 'initialize' do
+      assert @cluster
+    end
+
+    should 'generate cd-hit command' do
+      cmd = @cluster.generate_cdhit_command "assembly1.fasta", "output.fa"
+    end
+
+    should 'generate vsearch command' do
+      output = @cluster.generate_vsearch_command "assembly1.fasta", "output.txt"
+      a = "vsearch --cluster_fast assembly1.fasta --id 1.00 "
+      a << "--strand both --uc output.txt --threads 4"
+      b = output.split(" ")
+      b[0] = File.basename(b[0])
+      output = b.join(" ")
+      assert_equal a, output, "cmd"
+    end
+
+  end
+end

data/test/test_transfuse.rb

@@ -0,0 +1,107 @@
+#!/usr/bin/env	ruby
+
+require 'helper'
+require 'tmpdir'
+
+class TestTransfuse < Test::Unit::TestCase
+
+  context 'transfuse' do
+
+    setup do
+      @fuser = Transfuse::Transfuse.new 4
+    end
+
+    teardown do
+    end
+
+    should 'check for existence of files' do
+      list = []
+      list << File.join(File.dirname(__FILE__), 'data', 'assembly1.fasta')
+      list << File.join(File.dirname(__FILE__), 'data', 'assembly2.fasta')
+      files = @fuser.check_files list.join(",")
+      assert_equal 2, files.length, "length"
+    end
+
+    should "concatenate two files" do
+      list = []
+      list << File.join(File.dirname(__FILE__), 'data', 'assembly1.fasta')
+      list << File.join(File.dirname(__FILE__), 'data', 'assembly2.fasta')
+      Dir.mktmpdir do |tmpdir|
+        Dir.chdir(tmpdir) do
+          output = @fuser.concatenate list
+          assert File.exist?(output)
+          lines = `wc -l #{output}`
+          assert_equal 1000, lines.chomp.split.first.to_i
+        end
+      end
+    end
+
+    should "cluster fasta file" do
+      Dir.mktmpdir do |tmpdir|
+        Dir.chdir(tmpdir) do
+          file = File.join(File.dirname(__FILE__), 'data', 'assembly1.fasta')
+          hash = @fuser.cluster file
+          assert_equal 250, hash.size, "output size"
+        end
+      end
+    end
+
+    should "load scores from transrate output" do
+      files = []
+      files << File.join(File.dirname(__FILE__), 'data', 'contig_scores1.csv')
+      hash = @fuser.load_scores files
+      assert_equal 99, hash.size
+    end
+
+    should "filter contigs" do
+      files = []
+      scores = {}
+      files << File.join(File.dirname(__FILE__), 'data', 'assembly1.fasta')
+      scores["soap_contig173359"] = 1
+      scores["soap_contig38533"] = 0.5
+      scores["idba_contig44716"] = 0
+      new_list = @fuser.filter files, scores
+      assert_equal 1, new_list.length
+      cmd = "grep -c \">\" #{new_list.first}"
+      assert_equal 2, `#{cmd}`.chomp.split.first.to_i, "contigs"
+    end
+
+    should "run transrate on assembly files with reads" do
+      files = []
+      left = []
+      right = []
+      files << File.join(File.dirname(__FILE__), 'data', 'assembly3.fasta')
+      left << File.join(File.dirname(__FILE__), 'data', 'left.fq')
+      right << File.join(File.dirname(__FILE__), 'data', 'right.fq')
+      Dir.mktmpdir do |tmpdir|
+        Dir.chdir(tmpdir) do
+          scores = @fuser.transrate files, left, right
+          assert_equal 100, scores.size, "scores size"
+        end
+      end
+    end
+
+    should "select contigs" do
+      clusters = {"0" => ["contig1", "contig2"], "1" => ["contig3", "contig4"]}
+      scores = { "contig1" => 0.2,
+                 "contig2" => 0.3,
+                 "contig3" => 0.4,
+                 "contig4" => 0.2 }
+      best = @fuser.select_contigs clusters, scores
+      assert_equal 2, best.size
+      assert_equal "contig2", best[0]
+      assert_equal "contig3", best[1]
+    end
+
+    should "output contigs" do
+      best = ["soap_contig173359", "oases_contig80246"]
+      file = File.join(File.dirname(__FILE__), 'data', 'assembly1.fasta')
+      Dir.mktmpdir do |tmpdir|
+        Dir.chdir(tmpdir) do
+          @fuser.output_contigs best, file, "out"
+        end
+      end
+    end
+
+  end
+end

data/transfuse.gemspec

@@ -0,0 +1,29 @@
+
+require File.expand_path('../lib/transfuse/version', __FILE__)
+
+Gem::Specification.new do |gem|
+  gem.name        = 'transfuse'
+  gem.version     = Transfuse::VERSION::STRING.dup
+  gem.date        = '2015-05-22'
+  gem.summary     = "Merge assemblies"
+  gem.description = "See summary"
+  gem.authors     = ["Richard Smith-Unna", "Chris Boursnell"]
+  gem.email       = ['rds45@cam.ac.uk', 'cmb211@cam.ac.uk']
+  gem.files       = `git ls-files`.split("\n")
+  gem.executables = ["transfuse"]
+  gem.require_paths = %w( lib )
+  gem.homepage    = 'https://github.com/cboursnell/transfuse'
+  gem.license     = 'MIT'
+
+  gem.add_dependency 'trollop', '~> 2.0'
+  gem.add_dependency 'bio', '~> 1.4', '>= 1.4.3'
+  gem.add_dependency 'fixwhich', '~> 1.0', '>= 1.0.2'
+  gem.add_dependency 'bindeps', '~> 1.0', '>= 1.0.1'
+  gem.add_dependency 'transrate', '1.0.0.beta3'
+
+  gem.add_development_dependency 'rake', '~> 10.3', '>= 10.3.2'
+  gem.add_development_dependency 'turn', '~> 0.9', '>= 0.9.7'
+  gem.add_development_dependency 'simplecov', '~> 0.8', '>= 0.8.2'
+  gem.add_development_dependency 'shoulda-context', '~> 1.2', '>= 1.2.1'
+  gem.add_development_dependency 'coveralls', '~> 0.7'
+end

metadata

@@ -0,0 +1,249 @@
+--- !ruby/object:Gem::Specification
+name: transfuse
+version: !ruby/object:Gem::Version
+  version: 0.1.1
+platform: ruby
+authors:
+- Richard Smith-Unna
+- Chris Boursnell
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2015-05-22 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: trollop
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.0'
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.4'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.4.3
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.4'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.4.3
+- !ruby/object:Gem::Dependency
+  name: fixwhich
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.0'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.0.2
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.0'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.0.2
+- !ruby/object:Gem::Dependency
+  name: bindeps
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.0'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.0.1
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.0'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.0.1
+- !ruby/object:Gem::Dependency
+  name: transrate
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 1.0.0.beta3
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 1.0.0.beta3
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.3'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 10.3.2
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.3'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 10.3.2
+- !ruby/object:Gem::Dependency
+  name: turn
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.9'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.9.7
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.9'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.9.7
+- !ruby/object:Gem::Dependency
+  name: simplecov
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.8'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.8.2
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.8'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.8.2
+- !ruby/object:Gem::Dependency
+  name: shoulda-context
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.2'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.2.1
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.2'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.2.1
+- !ruby/object:Gem::Dependency
+  name: coveralls
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.7'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.7'
+description: See summary
+email:
+- rds45@cam.ac.uk
+- cmb211@cam.ac.uk
+executables:
+- transfuse
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- Gemfile
+- Gemfile.lock
+- README.md
+- Rakefile
+- bin/transfuse
+- deps/deps.yaml
+- lib/transfuse.rb
+- lib/transfuse/cluster.rb
+- lib/transfuse/cmd.rb
+- lib/transfuse/transfuse.rb
+- lib/transfuse/version.rb
+- notes.md
+- test/data/assembly1.fasta
+- test/data/assembly2.fasta
+- test/data/contig_scores1.csv
+- test/helper.rb
+- test/test_cluster.rb
+- test/test_transfuse.rb
+- transfuse.gemspec
+homepage: https://github.com/cboursnell/transfuse
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+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: 
+rubygems_version: 2.2.2
+signing_key: 
+specification_version: 4
+summary: Merge assemblies
+test_files: []