genome-pipeline 0.0.2 → 0.0.3

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: 09740883a700c684071a37504cebe596a8f4dfd2
+  data.tar.gz: 27c53736615681e04255de0f9b980320fa9a6463
+SHA512:
+  metadata.gz: 4cc2234b852349c146ae94b73b53787e535e499d1623b2ce66edf7459652eed281ebe66c0f9661d6bd1c73bd601aae4e7077721b6775a61beefda7446c33273a
+  data.tar.gz: e0e21d89d8156f741e626ad8f5fc8c24d5da4a00e70372b678df07c32ea8fcf3d8662a1bf23c930fc90303854cfe3790cb386437834309048d4da3d7155ca3dd

data/Gemfile

@@ -1,12 +1,12 @@
 source 'https://rubygems.org'
 
-gem 'dna'
-gem 'pry'
+gemspec
 
 group :development do
   gem 'rake'
   gem 'bundler'
   gem 'yard'
+  gem 'pry'
 end
 
 group :test do

data/genome-pipeline.gemspec

@@ -15,6 +15,8 @@ Gem::Specification.new do |gem|
   gem.test_files    = gem.files.grep(%r{^test})
   gem.require_paths = ["lib"]
 
+  gem.add_dependency 'dna', '~> 0.3.0'
+
   gem.cert_chain = ['certs/audy.cert']
   gem.signing_key = File.expand_path('~/.ssh/gem-private_key.pem') if $0 =~ /gem\z/
 

data/lib/genome/pipeline.rb

@@ -1,7 +1,3 @@
-require 'bundler'
-
-Bundler.require
-
 module Genome
 
   require 'genome/genome.rb'

data/lib/genome/pipeline/dummy_filter.rb

@@ -6,7 +6,7 @@ module Genome
 
     class DummyFilter < Filter
 
-      def transform
+      def call
         super
       end
 

data/lib/genome/pipeline/filter.rb

@@ -13,7 +13,7 @@ module Genome
         @genome = Marshal.load(Marshal.dump(genome))
       end
 
-      def transform
+      def call
         @genome.features << @result
         @genome
       end

data/lib/genome/pipeline/pipeline.rb

@@ -1,18 +1,22 @@
+require 'dna'
+
 module Genome
 
   class Pipeline
 
     attr_reader :steps
+    attr_reader :states
 
     def initialize *steps
       @steps = steps
+      @states = Array.new
     end
 
     def run genome
       @steps.each do |step|
-        genome = step.new(genome).transform
+        @states << step.new(genome).call
       end
-      return genome
+      @states.last
     end
 
 

data/lib/genome/pipeline/prodigal_filter.rb

@@ -5,7 +5,7 @@ module Genome
 
     class ProdigalFilter < Filter
 
-      def transform
+      def call
         @result = run_prodigal
         super
       end

data/lib/genome/pipeline/version.rb

@@ -1,5 +1,5 @@
 module Genome
   class Pipeline
-    VERSION = '0.0.2'
+    VERSION = '0.0.3'
   end
 end

data/readme.md

@@ -35,12 +35,8 @@ amino-acid coding sequences using Prodigal
 ```ruby
 class ProdigalFilter < Filter
 
-  attr_reader :result
-
   def transform
 
-    out_file = Tempfile.new 'prodigal'
-
     # run prodigal
     # read GFF and add add features to `genome`
     @result = 
@@ -49,8 +45,6 @@ class ProdigalFilter < Filter
         Features.from_gff(stdout.readlines)
       end
 
-    out_file.close
-
     super
   end
 end
@@ -70,9 +64,10 @@ feature finding software:
 
 - Augustus
 - tRNAscan
-- rnammer
-- snap
-- prokka
+- rnammer (closed source)
+- GeneMark (closed source)
+- snap (no Bacterial HMM)
+- prokka (see `add-prokka` branch)
 - barrnap
 - ARAGORN
 - repeatscout

data/spec/filter_spec.rb

@@ -9,8 +9,8 @@ describe Genome::Pipeline::Filter do
     expect(filter).to_not eq(nil)
   end
 
-  it '.transform should return a Genome' do
-    expect(filter.transform).to be_a(Genome::Genome)
+  it '.call should return a Genome' do
+    expect(filter.call).to be_a(Genome::Genome)
   end
 
   it 'can be created from Genome instance' do

data/spec/pipeline_spec.rb

@@ -7,7 +7,7 @@ describe Genome::Pipeline do
 
   let(:test_filter) do
     class TestFilter < Genome::Pipeline::Filter
-      def transform
+      def call
         @genome.features << 'a dummy feature'
       end
     end
@@ -18,7 +18,7 @@ describe Genome::Pipeline do
     expect(Genome::Pipeline).to_not eq(nil)
   end
 
-  it 'can perform transformations on a Genome' do
+  it 'can perform callations on a Genome' do
     expect { pipeline.run(genome) }.not_to raise_error
     expect(pipeline.run(genome)).to be_a(Genome::Genome)
   end
@@ -30,8 +30,13 @@ describe Genome::Pipeline do
 
   # this belongs in filter_spec
   it '.run should not alter original features' do
-    test_filter.new(genome).transform
+    test_filter.new(genome).call
     expect(genome.features.size).to eq(0)
   end
 
+  it '.run should save states' do
+    pipeline.run(genome)
+    expect(pipeline.states.size).to eq(1)
+  end
+
 end

data/spec/prodigal_filter_spec.rb

@@ -1,6 +1,5 @@
 require 'spec_helper'
 
-
 describe Genome::Pipeline::ProdigalFilter do
 
   let(:genome) { Genome::Genome.new(File.open('spec/data/genome.fasta')) }
@@ -11,11 +10,11 @@ describe Genome::Pipeline::ProdigalFilter do
     expect{filter}.not_to raise_error
   end
 
-  it '.transform' do
-    filtered_genome = filter.transform
+  it '.call' do
+    filtered_genome = filter.call
     expect(filtered_genome).to be_a(Genome::Genome)
     expect(filtered_genome.features).not_to eq(nil)
-    expect(filtered_genome.features.size).not_to eq(0)
+    expect(filtered_genome.features.compact.size).not_to eq(0)
   end
 
 end

metadata

@@ -1,43 +1,49 @@
 --- !ruby/object:Gem::Specification
 name: genome-pipeline
 version: !ruby/object:Gem::Version
-  version: 0.0.2
-  prerelease: 
+  version: 0.0.3
 platform: ruby
 authors:
 - Austin G. Davis-Richardson
 autorequire: 
 bindir: bin
 cert_chain:
-- !binary |-
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-  IENFUlRJRklDQVRFLS0tLS0K
-date: 2014-09-22 00:00:00.000000000 Z
-dependencies: []
+- |
+  -----BEGIN CERTIFICATE-----
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+  -----END CERTIFICATE-----
+date: 2014-09-23 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: dna
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.3.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.3.0
 description: Genome processing filters and utilities
 email:
 - harekrishna@gmail.com
@@ -45,9 +51,8 @@ executables: []
 extensions: []
 extra_rdoc_files: []
 files:
-- .gitignore
+- ".gitignore"
 - Gemfile
-- Gemfile.lock
 - Rakefile
 - certs/audy.cert
 - genome-pipeline.gemspec
@@ -72,36 +77,29 @@ files:
 homepage: https://github.com/audy/genome-pipeline
 licenses:
 - MIT
-post_install_message: ! '-------------------------------------------------
-
+metadata: {}
+post_install_message: |
+  -------------------------------------------------
   Thank you for installing genome-pipeline!
-
   -------------------------------------------------
-
-'
 rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
-      segments:
-      - 0
-      hash: 1582478238090731680
 required_rubygems_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.23.2
+rubygems_version: 2.2.2
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: Helpers for processing genomes through a chain of annotation filters
 test_files: []
 has_rdoc: 

data/Gemfile.lock

@@ -1,37 +0,0 @@
-GEM
-  remote: https://rubygems.org/
-  specs:
-    coderay (1.1.0)
-    diff-lcs (1.2.5)
-    dna (0.3.0)
-    method_source (0.8.2)
-    pry (0.10.0)
-      coderay (~> 1.1.0)
-      method_source (~> 0.8.1)
-      slop (~> 3.4)
-    rake (10.3.2)
-    rspec (3.1.0)
-      rspec-core (~> 3.1.0)
-      rspec-expectations (~> 3.1.0)
-      rspec-mocks (~> 3.1.0)
-    rspec-core (3.1.4)
-      rspec-support (~> 3.1.0)
-    rspec-expectations (3.1.1)
-      diff-lcs (>= 1.2.0, < 2.0)
-      rspec-support (~> 3.1.0)
-    rspec-mocks (3.1.1)
-      rspec-support (~> 3.1.0)
-    rspec-support (3.1.0)
-    slop (3.5.0)
-    yard (0.8.7.4)
-
-PLATFORMS
-  ruby
-
-DEPENDENCIES
-  bundler
-  dna
-  pry
-  rake
-  rspec
-  yard