genome-pipeline 0.0.1 → 0.0.2

data/.gitignore

@@ -0,0 +1 @@
+pkg/

data/Gemfile

@@ -6,6 +6,7 @@ gem 'pry'
 group :development do
   gem 'rake'
   gem 'bundler'
+  gem 'yard'
 end
 
 group :test do

data/Gemfile.lock

@@ -23,6 +23,7 @@ GEM
       rspec-support (~> 3.1.0)
     rspec-support (3.1.0)
     slop (3.5.0)
+    yard (0.8.7.4)
 
 PLATFORMS
   ruby
@@ -33,3 +34,4 @@ DEPENDENCIES
   pry
   rake
   rspec
+  yard

data/Rakefile

@@ -1,2 +1,14 @@
 require 'bundler/gem_tasks'
 require 'rake/testtask'
+
+Bundler.require :development
+
+namespace :docs do
+  YARD::Rake::YardocTask.new do |t|
+  end
+
+  desc 'serve documentation with live reloading'
+  task :serve do
+    `bundle exec yard server --reload`
+  end
+end

data/certs/audy.cert

@@ -0,0 +1,19 @@
+-----BEGIN CERTIFICATE-----
+MIIDIDCCAgigAwIBAgIBADANBgkqhkiG9w0BAQUFADA2MQowCAYDVQQDDAFfMRQw
+EgYKCZImiZPyLGQBGRYEYWdkcjESMBAGCgmSJomT8ixkARkWAmNvMB4XDTE0MDcw
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+hArlAbz8jIiZ5FhHecQVQ6Q0sDljNdFh5N6SQp9afYfJ0Dlb
+-----END CERTIFICATE-----

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.cert_chain = ['certs/audy.cert']
+  gem.signing_key = File.expand_path('~/.ssh/gem-private_key.pem') if $0 =~ /gem\z/
 
   gem.post_install_message = <<msg
 -------------------------------------------------

data/lib/genome/pipeline/dummy_filter.rb

@@ -0,0 +1,16 @@
+module Genome
+  class Pipeline
+
+    # dummy filter does nothing
+    # used for testing
+
+    class DummyFilter < Filter
+
+      def transform
+        super
+      end
+
+    end
+
+  end
+end

data/lib/genome/pipeline/filter.rb

@@ -9,15 +9,17 @@ module Genome
       attr_reader :result
 
       def initialize genome
-        @genome = genome
+        # store a deep copy of genome.
+        @genome = Marshal.load(Marshal.dump(genome))
       end
 
       def transform
+        @genome.features << @result
         @genome
       end
 
       def inspect
-        "#<#{self.class} #{@result} results genome=#{@genome}>"
+        "#<#{self.class} #{@result.size} results genome=#{@genome}>"
       end
 
     end

data/lib/genome/pipeline/pipeline.rb

@@ -1,6 +1,21 @@
 module Genome
 
-  module Pipeline
+  class Pipeline
+
+    attr_reader :steps
+
+    def initialize *steps
+      @steps = steps
+    end
+
+    def run genome
+      @steps.each do |step|
+        genome = step.new(genome).transform
+      end
+      return genome
+    end
+
+
   end
 
 end

data/lib/genome/pipeline/prodigal_filter.rb

@@ -1,28 +1,22 @@
-require 'tempfile'
+require 'open3'
 
 module Genome
   class Pipeline
 
     class ProdigalFilter < Filter
 
-      attr_reader :result
-
       def transform
+        @result = run_prodigal
+        super
+      end
 
-        out_file = Tempfile.new 'prodigal'
-
-        # run prodigal
-        # read GFF and add add features to `genome`
+      def run_prodigal
         @genome.fasta do |path|
-          `prodigal -f gff -i #{path} > #{out_file.path}`
+          stdin, stdout, stderr = Open3.popen3("prodigal -f gff -i #{path}")
+          Features.from_gff(stdout.readlines)
         end
-
-        @result = Features.from_gff(out_file)
-
-        out_file.close
-
-        super
       end
+
     end
 
   end

data/lib/genome/pipeline/version.rb

@@ -1,5 +1,5 @@
 module Genome
   class Pipeline
-    VERSION = '0.0.1'
+    VERSION = '0.0.2'
   end
 end

data/lib/genome/pipeline.rb

@@ -3,10 +3,13 @@ require 'bundler'
 Bundler.require
 
 module Genome
-  autoload :Genome, 'genome/genome.rb'
+
+  require 'genome/genome.rb'
+  require 'genome/pipeline/pipeline.rb'
 
   class Pipeline
     autoload :Filter, 'genome/pipeline/filter.rb'
+    autoload :DummyFilter, 'genome/pipeline/dummy_filter.rb'
     autoload :ProdigalFilter, 'genome/pipeline/prodigal_filter.rb'
   end
 

data/readme.md

@@ -1,6 +1,6 @@
 # Genome::Pipeline
 
-Annotate or do other things to Bacterial genomes.
+Genome processing filters and utilities
 
 Inspired by [HTML::Pipeline](https://github.com/jch/html-pipeline).
 
@@ -13,34 +13,76 @@ pipeline = Genome::Pipeline.new Filter::PRODIGAL,
 annotated_genome = pipeline[genome]
 ```
 
+# Installation
+
+With RubyGems:
+
+```bash
+$ gem install -P HighSecurity genome-pipeline
+```
+
+With Bundler:
+
+```ruby
+gem 'genome-pipeline', '~> 0.0.1'
+```
+
 ## Filters
 
 Pipelines are made up of filters. Here is a simple filter that predicts
 amino-acid coding sequences using Prodigal
 
 ```ruby
-require 'tempfile'
-
 class ProdigalFilter < Filter
 
   attr_reader :result
 
   def transform
+
     out_file = Tempfile.new 'prodigal'
 
     # run prodigal
     # read GFF and add add features to `genome`
-    @genome.fasta do |path|
-      `prodigal -f gff -i #{path} > #{out_file.path}`
-    end
+    @result = 
+      @genome.fasta do |path|
+        stdin, stdout, stderr = Open3.popen3("prodigal -f gff -i #{path}")
+        Features.from_gff(stdout.readlines)
+      end
 
-    @result = Features.from_gff(out_file)
+    out_file.close
 
     super
   end
 end
 ```
 
+## List of Filters
+
+### Gene Prediction
+
+- Prodigal [XX]
+
+### TODO
+
+feature finding software:
+
+(act on genome sequence)
+
+- Augustus
+- tRNAscan
+- rnammer
+- snap
+- prokka
+- barrnap
+- ARAGORN
+- repeatscout
+- repeatmasker
+- trf
+
+Filters that act on features:
+
+- Quality Filter (remove features below a confidence threshold)
+
 ## Genome Object
 
 Genomes are currently read from FASTA files and stored as objects. My future