genomer 0.0.5

data/lib/genomer/runtime.rb

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+require 'unindent'
+require 'tempfile'
+require 'ronn/index'
+require 'ronn/document'
+
+class Genomer::Runtime
+
+  attr :command
+  attr :arguments
+  attr :flags
+
+  def initialize(settings)
+    @command   = settings.rest.shift
+    @arguments = settings.rest
+    @flags     = settings
+  end
+
+  def execute!
+    case command
+    when nil    then short_help
+    when "help" then help
+    when "init" then init
+    when "man"  then man
+    else             run_plugin
+    end
+  end
+
+  def short_help
+    msg =<<-EOF
+      genomer COMMAND [options]
+      run `genomer help` for a list of available commands
+    EOF
+    msg.unindent
+  end
+
+  def help
+    msg =<<-EOF
+      genomer COMMAND [options]
+
+      Available commands:
+        init        Create a new genomer project
+        man         View man page for the specified plugin
+    EOF
+    msg.unindent!
+
+    msg << Genomer::Plugin.plugins.inject(String.new) do |str,p|
+      str << '  '
+      str << p.name.gsub("genomer-plugin-","").ljust(12)
+      str << p.summary
+      str << "\n"
+    end
+    msg.strip
+  end
+
+  def man
+    if not arguments.empty?
+      man_file_location = man_file(arguments.clone)
+      unless File.exists?(man_file_location)
+        raise Genomer::Error, "No manual entry for command '#{arguments.join(' ')}'"
+      end
+
+      Kernel.exec "man #{groffed_man_file(man_file_location).path}"
+    else
+      msg =<<-EOF
+        genomer man COMMAND
+        run `genomer help` for a list of available commands
+      EOF
+      msg.unindent!
+      msg.strip
+    end
+  end
+
+  def man_file(arguments)
+    plugin = arguments.first
+    page = arguments.unshift("genomer").join('-') << ".ronn"
+    File.join(Genomer::Plugin.fetch(plugin).full_gem_path, 'man', page)
+  end
+
+  def groffed_man_file(original_man_file)
+    converted_man = Tempfile.new("genome-manpage-")
+    File.open(converted_man.path,'w') do |out|
+      out.puts Ronn::Document.new(original_man_file).convert('roff')
+    end
+    converted_man
+  end
+
+  def init
+    project_name = arguments.first
+    if File.exists?(project_name)
+      raise Genomer::Error, "Directory '#{project_name}' already exists."
+    else
+      Dir.mkdir project_name
+      Dir.mkdir File.join(project_name,'assembly')
+    end
+  end
+
+  def run_plugin
+    Genomer::Plugin[command].new(arguments,flags).run
+  end
+
+end

data/lib/genomer/version.rb

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+module Genomer
+  VERSION = "0.0.5"
+end

data/man/genomer-init.1.ronn

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+genomer-init(1) -- create a new genomer project
+===============================================
+
+## SYNOPSIS
+
+`genomer init` <project-name>
+
+## DESCRIPTION
+
+Creates a new genomer project directory named **project-name**. Returns an
+error if the project directory already exists.
+
+## BUGS
+
+**Genomer-init** is written in Ruby and uses several RubyGems dependencies. See
+the Gemfile in the genomer gem install directory for version details.
+
+## COPYRIGHT
+
+**Genomer** is Copyright (C) 2011 Michael Barton <http://michaelbarton.me.uk>

data/spec/genomer/plugin_spec.rb

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+require 'spec_helper'
+
+describe Genomer::Plugin do
+
+  describe "#[]" do
+
+    before do
+      mock(described_class).plugins do
+        [Gem::Specification.new do |s|
+          s.name = 'genomer-plugin-simple'
+        end]
+      end
+    end
+
+    describe "fetching an available plugin" do
+
+      before do
+        mock(described_class).require('genomer-plugin-simple')
+      end
+
+      it "should return the class for this plugin" do
+        expected = GenomerPluginSimple = Class.new
+        described_class['simple'].should == expected
+      end
+
+    end
+
+    describe "fethcing an unavailble plugin" do
+
+      it "should print an error message" do
+        error =  "Unknown command or plugin 'unknown.'\n"
+        error << "run `genomer help` for a list of available commands\n"
+        lambda{ described_class['unknown'] }.should raise_error(Genomer::Error,error)
+      end
+
+    end
+
+  end
+
+  describe "#plugins" do
+
+    before do
+      mock(Bundler).setup do
+        mock!.gems{ gems }
+      end
+    end
+
+    describe "where a single genomer plugin is specified" do
+
+      let(:gems) do
+        [Gem::Specification.new do |s|
+          s.name = 'genomer-plugin-simple'
+        end]
+      end
+
+      it "should return the genomer plugin" do
+        described_class.plugins.should == gems
+      end
+
+    end
+
+    describe "where no gems at all are specified" do
+
+      let(:gems) do
+        []
+      end
+
+      it "should return an empty array" do
+        described_class.plugins.should be_empty
+      end
+
+    end
+
+    describe "where one plugin and one non-plugin are specified" do
+
+      let(:gems) do
+        [Gem::Specification.new{|s| s.name = 'genomer-plugin-simple' },
+         Gem::Specification.new{|s| s.name = 'not-a-plugin' }]
+      end
+
+      it "should return the genomer plugin" do
+        described_class.plugins.should == [gems.first]
+      end
+
+    end
+
+  end
+
+  describe "#to_class_name" do
+
+    it "should dash separated words to camel case" do
+      described_class.to_class_name('words-with-dashes').should == "WordsWithDashes"
+    end
+
+  end
+
+  describe "#scaffold" do
+
+    let(:entries) do
+      [Sequence.new(:name => 'seq1', :sequence => 'ATGC')]
+    end
+
+    let (:sequence_file) do
+      File.new("assembly/sequence.fna",'w')
+    end
+
+    let (:scaffold_file) do
+      File.new("assembly/scaffold.yml",'w')
+    end
+
+    before do
+      Dir.mkdir('assembly')
+      write_sequence_file(entries,sequence_file)
+      write_scaffold_file(entries,scaffold_file)
+    end
+
+    after do
+      FileUtils.rm_rf 'assembly'
+    end
+
+    subject do
+      described_class.new(nil,nil)
+    end
+
+    it "should return the expected scaffold built from the scaffold files" do
+      subject.scaffold.length.should == 1
+    end
+
+  end
+
+  describe "#annotations" do
+
+    before do
+      Dir.mkdir('assembly')
+      write_sequence_file(entries, File.new("assembly/sequence.fna",'w'))
+      write_scaffold_file(entries, File.new("assembly/scaffold.yml",'w'))
+      generate_gff3_file(records,  File.new("assembly/annotations.gff",'w'))
+    end
+
+    after do
+      FileUtils.rm_rf 'assembly'
+    end
+
+    let(:entries) do
+      [Sequence.new(:name => 'seq1', :sequence => 'ATGCATGCATGC')]
+    end
+
+    let(:annotation) do
+      Annotation.new(
+        :seqname    => 'seq1',
+        :start      => 1,
+        :end        => 3,
+        :feature    => 'gene',
+        :attributes => {'ID' => 'gene1'})
+    end
+
+    let(:options) do
+      {}
+    end
+
+    subject do
+      described_class.new(nil,nil).annotations(options)
+    end
+
+    describe "with no annotations" do
+
+      let(:records) do
+        []
+      end
+
+      it "should return one annotation entry" do
+        subject.length.should == 0
+      end
+
+    end
+
+    describe "with one annotation" do
+
+      let(:records) do
+        [annotation]
+      end
+
+      it "should return no annotations" do
+        subject.length.should == 1
+      end
+
+    end
+
+    describe "with one contig annotation and one non-contig annotation" do
+
+      let(:records) do
+        [annotation,annotation.clone.seqname('seq2')]
+      end
+
+      it "should return only the contig annotation" do
+        subject.length.should == 1
+      end
+
+    end
+
+    describe "with multiple unordered annotations" do
+
+      let(:records) do
+        [
+          annotation.clone.start(4).end(6),
+          annotation.clone.start(7).end(9),
+          annotation
+        ]
+      end
+
+      it "should return the annotations in order" do
+        subject[0].start.should == 1
+        subject[1].start.should == 4
+        subject[2].start.should == 7
+      end
+
+    end
+
+    describe "with the prefix option" do
+
+      let(:records) do
+        [annotation]
+      end
+
+      let(:options) do
+        {:prefix => 'pre_'}
+      end
+
+      it "should prefix the annotation id" do
+        subject.first.id.should == 'pre_gene1'
+      end
+
+    end
+
+    describe "with reset numbering" do
+
+      let(:records) do
+        [
+          annotation.clone.start(4).end(6),
+          annotation.clone.start(7).end(9),
+          annotation
+        ]
+      end
+
+      let(:options) do
+        {:reset => true}
+      end
+
+      it "should reset the locus tag numbering at 000001" do
+        subject[0].id.should == '000001'
+        subject[1].id.should == '000002'
+        subject[2].id.should == '000003'
+      end
+
+    end
+
+    describe "with reset numbering and an argument" do
+
+      let(:records) do
+        [
+          annotation.clone.start(4).end(6),
+          annotation.clone.start(7).end(9),
+          annotation
+        ]
+      end
+
+      let(:options) do
+        {:reset => '5'}
+      end
+
+      it "should reset the locus tag numbering starting at 000005" do
+        subject[0].id.should == '000005'
+        subject[1].id.should == '000006'
+        subject[2].id.should == '000007'
+      end
+
+    end
+
+    describe "with the reset numbering and prefix option" do
+
+      let(:records) do
+        [
+          annotation.clone.start(4).end(6),
+          annotation.clone.start(7).end(9),
+          annotation
+        ]
+      end
+
+      let(:options) do
+        {:reset => true, :prefix => 'pre_'}
+      end
+
+      it "should prefix and reset the locus tag numbering at 000001" do
+        subject[0].id.should == 'pre_000001'
+        subject[1].id.should == 'pre_000002'
+        subject[2].id.should == 'pre_000003'
+      end
+
+    end
+
+    describe "with reset numbering given an argument and the prefix option" do
+
+      let(:records) do
+        [
+          annotation.clone.start(4).end(6),
+          annotation.clone.start(7).end(9),
+          annotation
+        ]
+      end
+
+      let(:options) do
+        {:reset => '5', :prefix => 'pre_'}
+      end
+
+      it "should prefix and reset the locus tag numbering at 000005" do
+        subject[0].id.should == 'pre_000005'
+        subject[1].id.should == 'pre_000006'
+        subject[2].id.should == 'pre_000007'
+      end
+
+    end
+
+  end
+
+  describe "#initialize" do
+
+    subject do
+      described_class.new(:arguments,:flags)
+    end
+
+    it "should set the #arguments attribute" do
+      subject.arguments.should == :arguments
+    end
+
+    it "should set the #flags attribute" do
+      subject.arguments.should == :arguments
+    end
+
+  end
+
+end