genome-pipeline 0.0.1

data/spec/filter_spec.rb

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+require 'spec_helper'
+
+describe Genome::Pipeline::Filter do
+
+  let(:filter) { Genome::Pipeline::Filter.new(genome) }
+  let(:genome) { Genome::Genome.new(File.open('spec/data/genome.fasta')) }
+
+  it 'exists' do
+    expect(filter).to_not eq(nil)
+  end
+
+  it '.transform should return a Genome' do
+    expect(filter.transform).to be_a(Genome::Genome)
+  end
+
+  it 'can be created from Genome instance' do
+    expect(filter).to be_a(Genome::Pipeline::Filter)
+  end
+
+end

data/spec/genome_spec.rb

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+require 'spec_helper'
+
+describe Genome do
+
+  let (:fasta_handle) { File.open('spec/data/genome.fasta') }
+  let (:genome) { Genome::Genome.new(fasta_handle) }
+
+  it '.new' do
+    expect(genome).to_not eq(nil)
+  end
+
+  it '.fasta' do
+    genome.fasta do |path|
+      expect(path).to_not eq(nil)
+      expect(File.exist?(path)).to eq(true)
+
+      records = File.open(path) do |handle|
+        Dna.new(handle, format: :fasta).to_a
+      end
+
+      expect(records.size).not_to eq(0)
+      expect(`grep -c '^>' #{path}`).to eq(`grep -c '^>' 'spec/data/genome.fasta'`)
+    end
+  end
+
+end

data/spec/pipeline_spec.rb

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+require 'spec_helper'
+
+describe Genome::Pipeline do
+
+  it 'exists' do
+    expect(Genome::Pipeline).to_not eq(nil)
+  end
+
+end

data/spec/prodigal_filter_spec.rb

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+require 'spec_helper'
+
+
+describe Genome::Pipeline::ProdigalFilter do
+
+  let(:genome) { Genome::Genome.new(File.open('spec/data/genome.fasta')) }
+
+  let(:filter) { Genome::Pipeline::ProdigalFilter.new(genome) }
+
+  it '.new' do
+    expect{filter}.not_to raise_error
+  end
+
+  it '.transform' do
+    expect(filter.transform).to be_a(Genome::Genome)
+  end
+
+end

data/spec/spec_helper.rb

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+require 'bundler'
+Bundler.require :test
+
+require 'genome/pipeline'

metadata

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+--- !ruby/object:Gem::Specification
+name: genome-pipeline
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+  prerelease: 
+platform: ruby
+authors:
+- Austin G. Davis-Richardson
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2014-09-20 00:00:00.000000000 Z
+dependencies: []
+description: Genome processing filters and utilities
+email:
+- harekrishna@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- Gemfile
+- Gemfile.lock
+- Rakefile
+- genome-pipeline.gemspec
+- installation.md
+- lib/genome/genome.rb
+- lib/genome/genome/feature.rb
+- lib/genome/genome/genome.rb
+- lib/genome/pipeline.rb
+- lib/genome/pipeline/filter.rb
+- lib/genome/pipeline/pipeline.rb
+- lib/genome/pipeline/prodigal_filter.rb
+- lib/genome/pipeline/version.rb
+- readme.md
+- spec/data/genome.fasta
+- spec/data/prodigal.gff
+- spec/filter_spec.rb
+- spec/genome_spec.rb
+- spec/pipeline_spec.rb
+- spec/prodigal_filter_spec.rb
+- spec/spec_helper.rb
+homepage: https://github.com/audy/genome-pipeline
+licenses:
+- MIT
+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'
+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
+signing_key: 
+specification_version: 3
+summary: Helpers for processing genomes through a chain of annotation filters
+test_files: []