npsearch 0.0.1

data/test/test_np_search.rb

@@ -0,0 +1,122 @@
+#!/usr/bin/env ruby
+require 'coveralls'
+Coveralls.wear!
+
+require 'bio'
+require 'test/unit'
+
+require 'npsearch'
+require 'npsearch/arg_validator'
+
+class InputChanged
+  # Changed to include the full entry definition rather than just the id. This
+  # was necessary for when testing individual parts since this is changed in
+  # pipeline
+  def read(input_file)
+    input_read = {}
+    biofastafile = Bio::FlatFile.open(Bio::FastaFormat, input_file)
+    biofastafile.each_entry do |entry|
+      # entry.definition used instead of entry.id
+      input_read[entry.definition] = entry.seq
+    end
+    input_read
+  end
+end
+
+class UnitTests < Test::Unit::TestCase
+  def setup # read all expected files
+    @dir                  = 'test/files'
+    @translation_test     = NpSearch::Translation.new
+    @analysis_test        = NpSearch::Analysis.new
+    @test_input1          = InputChanged.new
+    @test_arg_vldr        = NpSearch::ArgValidators.new(:is_verbose)
+    @test_vldr            = NpSearch::Validators.new
+    @test_input_read      = NpSearch::Input.read("#{@dir}/genetic.fa")
+    @expected_translation = NpSearch::Input.read("#{@dir}/1_protein.fa")
+    @expected_orf         = NpSearch::Input.read("#{@dir}/2_orf.fa")
+    @expected_sp_out_file = File.read("#{@dir}/3_signalp_out.txt")
+    @expected_secretome   = @test_input1.read("#{@dir}/4_secretome.fa")
+    @expected_output      = @test_input1.read("#{@dir}/5_output.fa")
+    @motif                = 'KK|KR|RR|R..R|R....R|R......R|' \
+                            'H..R|H....R|H......R|K..R|K....R|K......R'
+    @motif_ar             = %w(KR Kr kr)
+    @input_file_ar        = ["#{@dir}/genetic.fa", "#{@dir}/protein.fa"]
+    @input_file_ar_neg    = ["#{@dir}/empty_file.fa",
+                             "#{@dir}/missing_input.fa", "#{@dir}/not_fasta.fa"]
+    @cut_off_ar           = [622, 10, 2, 1]
+    @cut_off_ar_neg       = [-10, 'hello', -5, 0]
+  end
+
+  def test_motif
+    (0..2).each do |i|
+      test_run = @test_arg_vldr.arg(@motif_ar[i], @input_file_ar[0], @dir,
+                                    @cut_off_ar[0], FALSE, nil, 'help_banner')
+      assert_equal('genetic', test_run)
+    end
+  end
+
+  def test_input_file
+    test_run = @test_arg_vldr.arg(@motif_ar[0], @input_file_ar[0], @dir,
+                                  @cut_off_ar[0], FALSE, nil, 'help_banner')
+    assert_equal('genetic', test_run)
+    test_run1 = @test_arg_vldr.arg(@motif_ar[0], @input_file_ar[1], @dir,
+                                   @cut_off_ar[0], FALSE, nil, 'help_banner')
+    assert_equal('protein', test_run1)
+    (0..2).each do |i|
+      test_run2 = lambda do
+        @test_arg_vldr.arg(@motif_ar[0], @input_file_ar_neg[i], @dir,
+                           @cut_off_ar[0], FALSE, nil, 'help_banner')
+      end
+      assert_raise(ArgumentError) { test_run2 }
+    end
+  end
+
+  def test_orf_min_length
+    (0..3).each do |i|
+      test_run = @test_arg_vldr.arg(@motif_ar[0], @input_file_ar[0], @dir,
+                                    @cut_off_ar[i], FALSE, nil, 'help_banner')
+      assert_equal('genetic', test_run)
+    end
+    (0..3).each do |i|
+      test_run1 = lambda do
+        @test_arg_vldr.arg(@motif_ar[0], @input_file_ar[0], @dir,
+                           @cut_off_ar_neg[i], FALSE, nil, 'help_banner')
+      end
+      assert_raise(ArgumentError) { test_run1 }
+    end
+  end
+
+  # => Test if the output directory validator works, in ensuring whether an
+  #    output directory can be found.
+  def test_output_dir_validator
+    assert_equal(nil, @test_vldr.output_dir(@dir))
+  end
+
+  # => Test if the translation method works properly - assert that the produced
+  #    translation is equal to the expected translation hash
+  def test_translate
+    translation_hash_test = NpSearch::Translation.translate(@test_input_read)
+    assert_equal(@expected_translation, translation_hash_test)
+  end
+
+  # => Test if the extract_orf method works properly - assert that the produced
+  #    orf hash is equal to the expected orf hash.
+  # => In orf method, an array is produced while in the expected file read, an
+  #    array isn't produced, thus it s necessary to remove "[  ]" from both end.
+  def test_extract_orf
+    orf_hash_test = NpSearch::Translation.extract_orf(@expected_translation, 10)
+    assert_equal(@expected_orf.to_s, orf_hash_test.to_s.gsub('["', '"')
+                                                       .gsub('"]', '"'))
+  end
+
+  def test_parse
+    secretome = NpSearch::Analysis.parse("#{@dir}/3_signalp_out.txt",
+                                         @expected_orf, @motif)
+    assert_equal(@expected_secretome, secretome)
+  end
+
+  def test_flattener
+    flattened_output_test = NpSearch::Analysis.flattener(@expected_secretome)
+    assert_equal(@expected_output, flattened_output_test)
+  end
+end

metadata

@@ -0,0 +1,162 @@
+--- !ruby/object:Gem::Specification
+name: npsearch
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+platform: ruby
+authors:
+- Ismail Moghul
+- Matthew Rowe
+- Anurag Priyam
+- Maurice Elphick
+- Yannick Wurm
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2015-09-13 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.6'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.6'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.3'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.3'
+- !ruby/object:Gem::Dependency
+  name: coveralls
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.4'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.4'
+- !ruby/object:Gem::Dependency
+  name: haml
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '4'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '4'
+description: Search for Neuropeptides based solely on the common neuropeptide markers
+  (e.g. signal peptide, dibasic cleavage sites etc.) i.e. not based on homology to
+  known neuropeptides.
+email:
+- y.wurm@qmul.ac.uk
+executables:
+- npsearch
+extensions: []
+extra_rdoc_files: []
+files:
+- ".coveralls.yml"
+- ".gitignore"
+- ".travis.yml"
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- bin/npsearch
+- lib/npsearch.rb
+- lib/npsearch/arg_validator.rb
+- lib/npsearch/logger.rb
+- lib/npsearch/pool.rb
+- lib/npsearch/sequence.rb
+- lib/npsearch/signalp.rb
+- lib/npsearch/version.rb
+- npsearch.gemspec
+- test/files/1_protein.fa
+- test/files/2_orf.fa
+- test/files/3_signalp_out.txt
+- test/files/4_secretome.fa
+- test/files/5_output.fa
+- test/files/5_output.html
+- test/files/empty_file.fa
+- test/files/genetic.fa
+- test/files/not_fasta.fa
+- test/files/protein.fa
+- test/files/signalp/signalp
+- test/test_np_search.rb
+homepage: https://github.com/IsmailM/NeuroPeptideSearch
+licenses:
+- AGPL
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: 2.0.0
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.4.8
+signing_key: 
+specification_version: 4
+summary: Search for neuropeptides based on the common neuropeptides markers
+test_files:
+- test/files/1_protein.fa
+- test/files/2_orf.fa
+- test/files/3_signalp_out.txt
+- test/files/4_secretome.fa
+- test/files/5_output.fa
+- test/files/5_output.html
+- test/files/empty_file.fa
+- test/files/genetic.fa
+- test/files/not_fasta.fa
+- test/files/protein.fa
+- test/files/signalp/signalp
+- test/test_np_search.rb
+has_rdoc: