genomer 0.0.5

data/features/api/scaffold.feature

@@ -0,0 +1,38 @@
+Feature: Plugins accessing the scaffold in a genomer project
+  In order to access the scaffold in a genomer plugin
+  A plugin developer can access the scaffold using the #scaffold method
+  So that the scaffold can be used
+
+  @disable-bundler
+  Scenario: Plugin accessing the scaffold
+    Given I run the genomer command with the arguments "init project"
+      And I cd to "project"
+      And I append to "Gemfile" with:
+      """
+      gem 'genomer',               :path => '../../../'
+      gem 'genomer-plugin-simple', :path => '../../../genomer-plugin-simple'
+      """
+      And I append to "assembly/scaffold.yml" with:
+      """
+      ---
+      -
+        sequence:
+          source: contig1
+      -
+        sequence:
+          source: contig2
+
+      """
+      And I append to "assembly/sequence.fna" with:
+      """
+      >contig1
+      ATGC
+      >contig2
+      ATGC
+      """
+     When I run the genomer command with the arguments "simple describe"
+     Then the exit status should be 0
+      And the output should contain:
+     """
+     The scaffold contains 2 entries
+     """

data/features/cli/create.feature

@@ -0,0 +1,19 @@
+Feature: Creating a new genomer project
+  In order to build a genome
+  A user can create a new genomer project
+  So that they can use the genomer commands and organise their data
+
+  Scenario: Creating a new project
+    When I run the genomer command with the arguments "init project"
+    Then the exit status should be 0
+    And a directory named "project" should exist
+    And a directory named "project/assembly" should exist
+
+  Scenario: Creating a new project where the directory already exists
+    Given a directory named "project"
+    When I run the genomer command with the arguments "init project"
+    Then the exit status should be 1
+    And the stderr should contain:
+    """
+    Error. Directory 'project' already exists.
+    """

data/features/cli/error.feature

@@ -0,0 +1,17 @@
+Feature: Reporting genomer errors
+  In order to use genomer correctly
+  A user can see descriptive genomer error messages
+  And understand how to correct the errors
+
+  Scenario: Calling a non-specified genomer plugin
+    Given I run the genomer command with the arguments "init project"
+      And I cd to "project"
+      And I append to "Gemfile" with ""
+     When I run the genomer command with the arguments "simple"
+     Then the exit status should be 1
+      And the output should contain:
+     """
+     Error. Unknown command or plugin 'simple.'
+     run `genomer help` for a list of available commands
+
+     """

data/features/cli/help.feature

@@ -0,0 +1,48 @@
+Feature: Listing available commands
+  In order to know which commands are available
+  A user can use the help command
+  To list the available options to the console
+
+  Scenario: Running genomer with no commands
+     When I run the genomer command with no arguments
+     Then the exit status should be 0
+      And the output should contain:
+     """
+     genomer COMMAND [options]
+     run `genomer help` for a list of available commands
+
+     """
+
+  Scenario: Running genomer with the help command
+     When I run the genomer command with the arguments "help"
+     Then the exit status should be 0
+      And the output should contain:
+     """
+     genomer COMMAND [options]
+
+     Available commands:
+     """
+      And the output should contain:
+     """
+       init        Create a new genomer project
+     """
+      And the output should contain:
+     """
+       man         View man page for the specified plugin
+     """
+
+  @disable-bundler
+  Scenario: Running help with a single genomer plugins specified
+    Given I run the genomer command with the arguments "init project"
+      And I cd to "project"
+      And I append to "Gemfile" with:
+      """
+      gem 'genomer-plugin-simple', :path => '../../../genomer-plugin-simple'
+      """
+     When I run the genomer command with the arguments "help"
+     Then the exit status should be 0
+      And the output should contain:
+     """
+       simple      Simple genomer plugin for testing purposes
+     """
+

data/features/cli/man.feature

@@ -0,0 +1,71 @@
+Feature: Showing man pages for available commands
+  In order to know which how to use genomer plugins
+  A user can use the man command
+  To show the man page for specified plugin
+
+  Scenario: Running genomer man with no commands
+     When I run the genomer command with the arguments "man"
+     Then the exit status should be 0
+      And the output should contain:
+      """
+      genomer man COMMAND
+      run `genomer help` for a list of available commands
+
+      """
+
+  @disable-bundler
+  Scenario: Getting the man page for a plugin
+    Given I run the genomer command with the arguments "init project"
+      And I cd to "project"
+      And I append to "Gemfile" with:
+      """
+      gem 'genomer-plugin-simple', :path => '../../../genomer-plugin-simple'
+      """
+     When I run the genomer command with the arguments "man simple"
+     Then the exit status should be 0
+      And the output should contain "GENOMER-SIMPLE(1)"
+
+  @disable-bundler
+  Scenario: Getting the man page for a plugin subcommand
+    Given I run the genomer command with the arguments "init project"
+      And I cd to "project"
+      And I append to "Gemfile" with:
+      """
+      gem 'genomer-plugin-simple', :path => '../../../genomer-plugin-simple'
+      """
+     When I run the genomer command with the arguments "man simple subcommand"
+     Then the exit status should be 0
+     And the output should contain "GENOMER-SIMPLE-SUBCOMMAND(1)"
+
+  @disable-bundler
+  Scenario: Trying to get a man page for an unknown plugin
+    Given I run the genomer command with the arguments "init project"
+      And I cd to "project"
+      And I append to "Gemfile" with:
+      """
+      gem 'genomer-plugin-simple', :path => '../../../genomer-plugin-simple'
+      """
+     When I run the genomer command with the arguments "man unknown"
+     Then the exit status should be 1
+      And the output should contain:
+      """
+      Error. Unknown command or plugin 'unknown.'
+      run `genomer help` for a list of available commands
+
+      """
+
+  @disable-bundler
+  Scenario: Trying to get a man page for an unknown subcommand
+    Given I run the genomer command with the arguments "init project"
+      And I cd to "project"
+      And I append to "Gemfile" with:
+      """
+      gem 'genomer-plugin-simple', :path => '../../../genomer-plugin-simple'
+      """
+     When I run the genomer command with the arguments "man simple unknown"
+     Then the exit status should be 1
+      And the output should contain:
+      """
+      Error. No manual entry for command 'simple unknown'
+
+      """

data/features/cli/plugins.feature

@@ -0,0 +1,34 @@
+Feature: Calling genomer plugins in a genomer project
+  In order to use third-party genomer plugins
+  A user can specify genomer plugins in a Gemfile
+  And call these plugins on the command line
+
+  @disable-bundler
+  Scenario: Calling a genomer plugin with no command
+    Given I run the genomer command with the arguments "init project"
+      And I cd to "project"
+      And I append to "Gemfile" with:
+      """
+      gem 'genomer-plugin-simple', :path => '../../../genomer-plugin-simple'
+      """
+     When I run the genomer command with the arguments "simple"
+     Then the exit status should be 0
+      And the output should contain:
+     """
+     Plugin "simple" called
+     """
+
+  @disable-bundler
+  Scenario: Calling a genomer plugin with a command
+    Given I run the genomer command with the arguments "init project"
+      And I cd to "project"
+      And I append to "Gemfile" with:
+      """
+      gem 'genomer-plugin-simple', :path => '../../../genomer-plugin-simple'
+      """
+     When I run the genomer command with the arguments "simple echo some words"
+     Then the exit status should be 0
+      And the output should contain:
+     """
+     Echo: some words
+     """

data/features/step_definitions/genomer_steps.rb

@@ -0,0 +1,10 @@
+GENOMER = File.join %W|#{File.dirname(__FILE__)} .. .. bin genomer|
+
+Given /^I run the genomer command with the arguments "([^"]*)"$/ do |args|
+  step "I run `#{GENOMER} #{args}`"
+end
+
+Given /^I run the genomer command with no arguments/ do
+  step 'I run the genomer command with the arguments ""'
+end
+

data/features/support/env.rb

@@ -0,0 +1,13 @@
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+
+$LOAD_PATH.unshift(File.dirname(__FILE__) + '/../../lib')
+$LOAD_PATH.unshift(File.dirname(__FILE__) + '/../../spec')
+
+require 'aruba/cucumber'

data/genomer-plugin-simple/genomer-plugin-simple.gemspec

@@ -0,0 +1,18 @@
+Gem::Specification.new do |s|
+  s.name        = "genomer-plugin-simple"
+  s.version     = "0.0.0"
+  s.platform    = Gem::Platform::RUBY
+  s.authors     = ["Michael Barton"]
+  s.email       = ["mail@michaelbarton.me.uk"]
+  s.homepage    = "http://next.gs"
+  s.summary     = "Simple genomer plugin for testing purposes"
+  s.description = "Empty"
+
+  s.required_rubygems_version = ">= 1.8"
+
+  # required for validation
+  s.rubyforge_project         = "genomer-plugin-simple"
+
+  s.files        = Dir["{lib}/**/*.rb"]
+  s.require_path = 'lib'
+end

data/genomer-plugin-simple/lib/genomer-plugin-simple.rb

@@ -0,0 +1,19 @@
+class GenomerPluginSimple < Genomer::Plugin
+
+  def run
+    case arguments.shift
+    when nil           then 'Plugin "simple" called'
+    when 'echo'        then "Echo: #{arguments.join(' ')}"
+    when 'describe'    then "The scaffold contains #{scaffold.length} entries"
+    when 'annotations' then annotations
+    end
+  end
+
+  def annotations
+    args = Hash.new
+    args[:prefix] = flags[:prefix] if flags[:prefix]
+    args[:reset]  = flags[:reset_locus_numbering] if flags[:reset_locus_numbering]
+    super(args).inject("##gff-version 3\n"){|s, a| s << a.to_s}
+  end
+
+end

data/genomer-plugin-simple/man/genomer-simple-subcommand.ronn

@@ -0,0 +1,6 @@
+genomer-simple-subcommand(1) -- A test plugin subcommand
+========================================================
+
+## SYNOPSIS
+
+`genomer simple subcommand`

data/genomer-plugin-simple/man/genomer-simple.ronn

@@ -0,0 +1,6 @@
+genomer-simple(1) -- A test plugin for genomer
+==============================================
+
+## SYNOPSIS
+
+`genomer simple`

data/genomer.gemspec

@@ -0,0 +1,39 @@
+# -*- encoding: utf-8 -*-
+require File.expand_path("../lib/genomer/version", __FILE__)
+
+Gem::Specification.new do |s|
+  s.name        = "genomer"
+  s.version     = Genomer::VERSION
+  s.platform    = Gem::Platform::RUBY
+  s.authors     = ["Michael Barton"]
+  s.email       = ["mail@michaelbarton.me.uk"]
+  s.homepage    = "http://github.com/michaelbarton/genomer"
+  s.summary     = %Q{Build genome output files}
+  s.description = %Q{Turns scaffolded contigs and annotations into a genome.}
+  s.license     = "MIT"
+
+  s.required_rubygems_version = ">= 1.8.0"
+  s.rubyforge_project         = "genomer"
+
+  s.add_dependency "rake",                          "~> 0.9.0"
+  s.add_dependency "bundler",                       "~> 1.1.0"
+  s.add_dependency "configliere",                   "~> 0.4.8"
+  s.add_dependency "scaffolder",                    "~> 0.4.0"
+  s.add_dependency "scaffolder-annotation-locator", ">= 0.1.2"
+  s.add_dependency "unindent",                      "~> 1.0.0"
+  s.add_dependency "ronn",                          "~> 0.7.3"
+
+  # Specs
+  s.add_development_dependency "rspec",                   "~> 2.7.0"
+  s.add_development_dependency "fakefs",                  "~> 0.4.0"
+  s.add_development_dependency "rr",                      "~> 1.0.4"
+  s.add_development_dependency "scaffolder-test-helpers", "~> 0.4.0"
+
+  # Features
+  s.add_development_dependency "cucumber", "~> 1.1.4"
+  s.add_development_dependency "aruba",    "~> 0.4.11"
+
+  s.files        = `git ls-files`.split("\n")
+  s.executables  = `git ls-files`.split("\n").map{|f| f =~ /^bin\/(.*)/ ? $1 : nil}.compact
+  s.require_path = 'lib'
+end

data/lib/genomer.rb

@@ -0,0 +1,6 @@
+module Genomer
+  require 'genomer/error'
+
+  autoload :Runtime, 'genomer/runtime'
+  autoload :Plugin,  'genomer/plugin'
+end

data/lib/genomer/error.rb

@@ -0,0 +1,4 @@
+module Genomer
+  class Error < StandardError
+  end
+end

data/lib/genomer/plugin.rb

@@ -0,0 +1,126 @@
+require 'scaffolder'
+require 'scaffolder/annotation_locator'
+
+# Superclass for genomer plugins which us the genomer plugin. This class
+# implements the common API which plugins should use to interact with the
+# genomer system
+class Genomer::Plugin
+
+  # Return the corresponding class for this plugin name.
+  #
+  # This method calls {Kernel#require} for the requested plugin by searching
+  # the available plugins for genomer-plugin-NAME. Where name is the passed
+  # string. The class for this plugin is then returned.
+  #
+  # @param [String] name The name of plugin without the 'genomer-plugin-' prefix.
+  # @return [Class] The class for this genomer plugin.
+  def self.[](plugin)
+    name = fetch(plugin).name
+    require name
+    Kernel.const_get(to_class_name(name))
+  end
+
+  def self.fetch(name)
+    plugin = plugins.detect{|i| i.name == "genomer-plugin-#{name}" }
+    unless plugin 
+      error =  "Unknown command or plugin '#{name}.'\n"
+      error << "run `genomer help` for a list of available commands\n"
+      raise Genomer::Error, error
+    end
+    plugin
+  end
+
+  private
+
+  # All the avaiable gems with a matching genomer-plugin- prefix.
+  #
+  # @return [Array] An array of genomer plugin gems
+  def self.plugins
+    require 'bundler'
+    Bundler.setup.gems.select{|gem| gem.name =~ /genomer-plugin-.+/ }
+  end
+
+  # Convert hyphen separated list of words to camel case
+  #
+  # @param [String] Hyphen separate string
+  # @return [String] Camel case string
+  def self.to_class_name(string)
+    string.split('-').map{|i| i.capitalize}.join
+  end
+
+  public
+
+  # @return [Array] List of command line arguments
+  attr :arguments
+
+  # @return [Hash] Command line flags as where --flag=value is :flag => value
+  attr :flags
+
+  attr :sequence_file
+  attr :scaffold_file
+  attr :annotation_file
+
+  # Initialize plugin with passed command line parameters.
+  #
+  # This create a plugin instance with the command line arguments and instance set as
+  # instance variables. These command line arguments are passed by the
+  # Genomer::Runtime.
+  #
+  # @param [Array] arguments List of command arguments
+  # @param [Hash] settings Command line flags as :flag => value
+  def initialize(arguments,flags)
+    @arguments = arguments
+    @flags     = flags
+
+    assembly = Pathname.new('assembly')
+    @sequence_file   = assembly + 'sequence.fna'
+    @scaffold_file   = assembly + 'scaffold.yml'
+    @annotation_file = assembly + 'annotations.gff'
+  end
+
+  # The genome scaffold constructed from the files in the "ROOT/assembly/" directory.
+  #
+  # @return [Array] An array of Scaffolder::Region instances
+  def scaffold
+    YAML::ENGINE.yamler = 'syck'
+    Scaffolder.new(YAML.load(File.read(scaffold_file)),sequence_file)
+  end
+
+  def annotations(options = {})
+    attns = Scaffolder::AnnotationLocator.new(
+      scaffold_file,sequence_file,annotation_file)
+
+    attns.sort_by! do |attn|
+      [attn.start,attn.end]
+    end
+
+    if value = options[:reset]
+      start = value.to_s =~ /^[-+]?[0-9]+$/ ? value.to_i : 1
+
+      genes = attns.select{|i| i.feature == 'gene'}
+      genes.each_with_index do |annotation,count|
+        annotation.id.replace sprintf("%06d",count + start)
+      end
+    end
+
+    if prefix = options[:prefix]
+      genes = attns.select{|i| i.feature == 'gene'}
+      genes.each{|attn| attn.id.insert(0,prefix) }
+    end
+
+    attns
+  end
+
+  # This method should be overriden to perform this plugin's operation.
+  #
+  # The run method is called on the plugin by Genomer::Runtime. This should be
+  # overridden in subclasses to perform the intended function. If an error is
+  # encountered raise a Genomer::Error with a description. This will be caught
+  # and the error message printed to the standard out.
+  #
+  # @return [String] The string output of this plugin. This is
+  # subsequently output to the command line
+  def run
+  end
+
+end