scaffolder-tools 0.1.0

data/.document

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+README.rdoc
+lib/**/*.rb
+bin/*
+features/**/*.feature
+LICENSE

data/.rspec

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+--color

data/Gemfile

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+source "http://rubygems.org"
+
+group :default do
+  gem "configliere", "~> 0.1"
+  gem "bio",         "~> 1.4"
+  gem "scaffolder",  "~> 0.4"
+  gem "ronn",        "~> 0.7"
+end
+
+group :development do
+  gem "bundler",  "~> 1.0"
+  gem "jeweler",  "~> 1.5"
+  gem "gherkin",  "~> 2.3.3"
+  gem "rspec",    "~> 2.4"
+  gem "cucumber", "~> 0.10"
+  gem "fakefs",   "~> 0.2"
+  gem "aruba",    "~> 0.2"
+  gem "mocha",    "~> 0.9"
+  gem "hashie",   "~> 0.4"
+  gem "yard",     "~> 0.6"
+
+  gem "scaffolder-test-helpers", "~> 0.1"
+end

data/LICENSE.txt

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+Copyright (c) 2010 Michael Barton
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.rdoc

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+== Synopsis
+
+A command line tool for processing genome scaffolds defined by the genome
+scaffolder API.
+
+== Feature List
+
+* Output scaffold to fasta format.
+* Test inserts do not overlap in the scaffold.
+
+== Installing
+
+Ruby and RubyGems are required to use scaffolder. Scaffolder tools is
+installed on the command line using:
+
+  $ gem install scaffolder-tools
+
+== Documentation
+
+Command line usage can be found by running the following:
+
+  $ scaffolder help
+
+A unix man page is available for each scaffolder command by typing:
+
+  $ scaffolder help COMMAND
+
+== Contact
+
+Scaffolder was developed by Michael Barton (http://www.michaelbarton.me.uk).
+Pull requests, patches and bug reports are welcome. The source code is
+available on github[http://github.com/michaelbarton/scaffolder]. Bug reports
+and feature requests should be made here.
+
+== Copyright
+
+Scaffolder © 2010 by Michael Barton. Scaffolder is licensed under the MIT
+license. Please see the LICENSE document for more information.

data/Rakefile

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+require 'rubygems'
+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
+require 'rake'
+
+require 'jeweler'
+Jeweler::Tasks.new do |gem|
+  gem.name = "scaffolder-tools"
+  gem.summary = "Tools for manipulating genome scaffolds"
+  gem.description = "Binary to use with scaffolder genome scaffolds"
+  gem.email = "mail@michaelbarton.me.uk"
+  gem.homepage = "http://github.com/michaelbarton/scaffolder-tools"
+  gem.authors = ["Michael Barton"]
+  gem.license = "MIT"
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+require 'rspec/core'
+require 'rspec/core/rake_task'
+RSpec::Core::RakeTask.new(:spec) do |spec|
+  spec.pattern = FileList['spec/**/*_spec.rb']
+end
+
+RSpec::Core::RakeTask.new(:rcov) do |spec|
+  spec.pattern = 'spec/**/*_spec.rb'
+  spec.rcov = true
+end
+
+require 'cucumber/rake/task'
+Cucumber::Rake::Task.new(:features)
+
+task :default => :spec
+
+require 'yard'
+YARD::Rake::YardocTask.new

data/VERSION

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+0.1.0

data/bin/scaffolder

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+#!/usr/bin/env ruby
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+
+require 'rubygems'
+require 'configliere'
+require 'scaffolder/binary_helper'
+
+extend Scaffolder::BinaryHelper
+
+Settings.use :commandline
+Settings.resolve!
+
+tool, arguments = determine_tool(Settings)
+tool.new(arguments).run

data/features/help.feature

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+Feature: Command line help for scaffolder
+  In order to understand how the scaffolder tools work
+  A user can use scaffolder help at the command line
+  to review its documentation
+
+  Scenario: Running scaffolder without any arguments
+    When I call "scaffolder" with arguments ""
+    Then the exit status should be 0
+    And the stdout should contain exactly:
+    """
+    usage: scaffolder [--version] COMMAND scaffold-file sequence-file
+    [options]
+
+    Commands:
+      help        Help information for scaffolder commands
+      sequence    Generate the fasta output for the scaffold
+      validate    Validate scaffold for overlapping inserts
+
+    """
+
+  Scenario: Running scaffolder with the version argument
+    When I call "scaffolder" with arguments "--version"
+    Then the exit status should be 0
+    And the stdout should contain exactly:
+    """
+    scaffolder tool version 0.1.0
+
+    """
+
+  Scenario: Running scaffolder with an incorrect command
+    When I call "scaffolder" with arguments "unknown-command"
+    Then the exit status should be 1
+    And the stderr should contain exactly:
+    """
+    Error. Unknown command 'unknown-command'.
+    See 'scaffolder help'.
+
+    """
+
+  Scenario: Running scaffolder with just the help argument
+    When I call "scaffolder" with arguments "help"
+    Then the exit status should be 0
+    And the stdout should contain exactly:
+    """
+    usage: scaffolder [--version] COMMAND scaffold-file sequence-file
+    [options]
+
+    Commands:
+      help        Help information for scaffolder commands
+      sequence    Generate the fasta output for the scaffold
+      validate    Validate scaffold for overlapping inserts
+
+    """
+
+  Scenario: Fetching the man page for sequence
+    When I call "scaffolder" with arguments "help sequence"
+    Then the exit status should be 0
+    And the stdout should contain "SCAFFOLDER-SEQUENCE(1)"
+
+  Scenario: Fetching the man page for validate
+    When I call "scaffolder" with arguments "help validate"
+    Then the exit status should be 0
+    And the stdout should contain "SCAFFOLDER-VALIDATE(1)"
+
+  Scenario: Fetching the man page for help
+    When I call "scaffolder" with arguments "help help"
+    Then the exit status should be 0
+    And the stdout should contain "SCAFFOLDER-HELP(1)"
+
+  Scenario: Fetching the man page for an incorrect command
+    When I call "scaffolder" with arguments "help unknown-command"
+    Then the exit status should be 1
+    And the stderr should contain exactly:
+    """
+    Error. Unknown command 'unknown-command'.
+    See 'scaffolder help'.
+
+    """
+

data/features/sequence.feature

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+Feature: The scaffolder-sequence binary
+  In order to generate a fasta sequence of a genome scaffold
+  A user can use the scaffolder binary with argument sequence
+  to generate a fasta sequence from a scaffold and sequence file
+
+  Scenario: Generating fasta sequence for a simple scaffold
+    Given a file named "sequence.fna" with:
+      """
+      >seq
+      ATGGC
+      """
+    Given a file named "scaffold.yml" with:
+      """
+      ---
+        -
+          sequence:
+            source: "seq"
+      """
+    When I call "scaffolder" with arguments "sequence scaffold.yml sequence.fna"
+    Then the exit status should be 0
+    And the stdout should contain "ATGGC"
+
+  Scenario: The sequence file specified does not exist
+    Given a file named "scaffold.yml" with:
+      """
+      ---
+        -
+          sequence:
+            source: "seq"
+      """
+    When I call "scaffolder" with arguments "sequence scaffold.yml missing_file"
+    Then the exit status should be 1
+    And the stderr should contain "Error. Sequence file not found:"
+
+  Scenario: The sequence file doesn't contain any thing
+    Given an empty file named "sequence.fna"
+    Given a file named "scaffold.yml" with:
+      """
+      ---
+        -
+          sequence:
+            source: "seq1"
+      """
+    When I call "scaffolder" with arguments "sequence scaffold.yml sequence.fna"
+    Then the exit status should be 1
+    And the stderr should contain "Error. Sequence file is empty"
+
+  Scenario: The scaffold file specified does not exist
+    Given a file named "sequence.fna" with:
+      """
+      >seq
+      ATGGC
+      """
+    When I call "scaffolder" with arguments "sequence missing_file sequence.fna"
+    Then the exit status should be 1
+    And the stderr should contain "Error. Scaffold file not found:"
+
+  Scenario: The scaffold file doesn't contain anything
+    Given an empty file named "scaffold.yml"
+    Given a file named "sequence.fna" with:
+      """
+      >seq
+      ATGGC
+      """
+    When I call "scaffolder" with arguments "sequence scaffold.yml sequence.fna"
+    Then the exit status should be 1
+    And the stderr should contain "Error. Scaffold file is empty"
+
+  Scenario: One of the sequences specified in the scaffold is missing
+    Given a file named "sequence.fna" with:
+      """
+      >seq1
+      ATGGC
+      """
+    Given a file named "scaffold.yml" with:
+      """
+      ---
+        -
+          sequence:
+            source: "seq1"
+        -
+          sequence:
+            source: "seq2"
+      """
+    When I call "scaffolder" with arguments "sequence scaffold.yml sequence.fna"
+    Then the exit status should be 1
+    And the stderr should contain "Error. Unknown sequence: seq2"
+
+  Scenario: Using the definition argument before the file arguments
+    Given a file named "sequence.fna" with:
+      """
+      >seq
+      ATGGC
+      """
+    Given a file named "scaffold.yml" with:
+      """
+      ---
+        -
+          sequence:
+            source: "seq"
+      """
+    When I call "scaffolder" with arguments "sequence --definition='name' scaffold.yml sequence.fna"
+    Then the exit status should be 0
+    And the stdout should contain "ATGGC"
+    And the stdout should contain ">name"
+
+  Scenario: Using the definition argument after the file arguments
+    Given a file named "sequence.fna" with:
+      """
+      >seq
+      ATGGC
+      """
+    Given a file named "scaffold.yml" with:
+      """
+      ---
+        -
+          sequence:
+            source: "seq"
+      """
+    When I call "scaffolder" with arguments "sequence scaffold.yml sequence.fna --definition='name'"
+    Then the exit status should be 0
+    And the stdout should contain "ATGGC"
+    And the stdout should contain ">name"
+
+  Scenario: Using the argument --no-sequence-hash
+    Given a file named "sequence.fna" with:
+      """
+      >seq
+      ATGGC
+      """
+    Given a file named "scaffold.yml" with:
+      """
+      ---
+        -
+          sequence:
+            source: "seq"
+      """
+    When I call "scaffolder" with arguments "sequence --no-sequence-hash scaffold.yml sequence.fna"
+    Then the exit status should be 0
+    And the stdout should contain ">\nATGGC"
+
+  Scenario: Using the arguments --no-sequence-hash and --definition
+    Given a file named "sequence.fna" with:
+      """
+      >seq
+      ATGGC
+      """
+    Given a file named "scaffold.yml" with:
+      """
+      ---
+        -
+          sequence:
+            source: "seq"
+      """
+      When I call "scaffolder" with arguments "sequence scaffold.yml sequence.fna --no-sequence-hash --definition='name'"
+    Then the exit status should be 0
+    And the stdout should contain ">name \nATGGC"

data/features/step_definitions/scaffolder-tools.rb

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+When /^I call "([^"]*)" with arguments "([^"]*)"$/ do |command,args|
+  bin = File.join(File.dirname(__FILE__),'..','..','bin',command)
+  When "I run \"#{bin} #{args}\""
+end

data/features/support/env.rb

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+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
+
+require 'rspec/expectations'
+require 'aruba/cucumber'
+
+Before do
+  @dirs = ["/tmp"]
+end

data/features/validate.feature

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+Feature: The scaffolder-validate binary
+  In order to test inserts are being correctly added to a scaffold
+  A user can use the scaffolder binary with the argument validate
+  to test that inserts are correctly inserted
+
+  Scenario: The sequence file specified does not exist
+    Given a file named "scaffold.yml" with:
+      """
+      ---
+        -
+          sequence:
+            source: "seq"
+      """
+    When I call "scaffolder" with arguments "validate scaffold.yml missing_file"
+    Then the exit status should be 1
+    And the stderr should contain "Error. Sequence file not found:"
+
+  Scenario: The sequence file doesn't contain any thing
+    Given an empty file named "sequence.fna"
+    Given a file named "scaffold.yml" with:
+      """
+      ---
+        -
+          sequence:
+            source: "seq1"
+      """
+    When I call "scaffolder" with arguments "validate scaffold.yml sequence.fna"
+    Then the exit status should be 1
+    And the stderr should contain "Error. Sequence file is empty"
+
+  Scenario: The scaffold file specified does not exist
+    Given a file named "sequence.fna" with:
+      """
+      >seq
+      ATGGC
+      """
+    When I call "scaffolder" with arguments "validate missing_file sequence.fna"
+    Then the exit status should be 1
+    And the stderr should contain "Error. Scaffold file not found:"
+
+  Scenario: The scaffold file doesn't contain anything
+    Given an empty file named "scaffold.yml"
+    Given a file named "sequence.fna" with:
+      """
+      >seq
+      ATGGC
+      """
+    When I call "scaffolder" with arguments "validate scaffold.yml sequence.fna"
+    Then the exit status should be 1
+    And the stderr should contain "Error. Scaffold file is empty"
+
+  Scenario: One of the sequences specified in the scaffold is missing
+    Given a file named "sequence.fna" with:
+      """
+      >seq1
+      ATGGC
+      """
+    Given a file named "scaffold.yml" with:
+      """
+      ---
+        -
+          sequence:
+            source: "seq1"
+        -
+          sequence:
+            source: "seq2"
+      """
+    When I call "scaffolder" with arguments "validate scaffold.yml sequence.fna"
+    Then the exit status should be 1
+    And the stderr should contain "Error. Unknown sequence: seq2"
+
+  Scenario: Validating a scaffold with no overlapping inserts
+    Given a file named "sequence.fna" with:
+      """
+      >seq
+      ATGGC
+      """
+    Given a file named "scaffold.yml" with:
+      """
+      ---
+        -
+          sequence:
+            source: "seq"
+      """
+    When I call "scaffolder" with arguments "validate scaffold.yml sequence.fna"
+    Then the exit status should be 0
+    And the stdout should contain exactly:
+    """
+    """
+
+  Scenario: Validating a scaffold with no inserts
+    Given a file named "sequence.fna" with:
+      """
+      >seq
+      ATGGC
+      """
+    Given a file named "scaffold.yml" with:
+      """
+      ---
+        -
+          sequence:
+            source: "seq"
+      """
+    When I call "scaffolder" with arguments "validate scaffold.yml sequence.fna"
+    Then the exit status should be 0
+    And the stdout should contain exactly:
+    """
+    """
+
+  Scenario: Validating a scaffold with two non-overlapping inserts
+    Given a file named "sequence.fna" with:
+      """
+      >seq
+      ATGGCG
+      >ins1
+      ATGGCG
+      >ins2
+      ATGGCG
+      """
+    Given a file named "scaffold.yml" with:
+      """
+      ---
+        -
+          sequence:
+            source: "seq"
+            inserts:
+            -
+              open: 2
+              close: 3
+              source: ins1
+            -
+              open: 4
+              close: 5
+              source: ins2
+
+      """
+    When I call "scaffolder" with arguments "validate scaffold.yml sequence.fna"
+    Then the exit status should be 0
+    And the stdout should contain exactly:
+    """
+    """
+
+  Scenario: Validating a scaffold with two overlapping inserts
+    Given a file named "sequence.fna" with:
+      """
+      >seq
+      ATGGCG
+      >ins1
+      ATGGCG
+      >ins2
+      ATGGCG
+      """
+    Given a file named "scaffold.yml" with:
+      """
+      ---
+        -
+          sequence:
+            source: "seq"
+            inserts:
+            -
+              open: 2
+              close: 4
+              source: ins1
+            -
+              open: 3
+              close: 5
+              source: ins2
+
+      """
+    When I call "scaffolder" with arguments "validate scaffold.yml sequence.fna"
+    Then the exit status should be 0
+    And the stdout should contain exactly:
+    """
+    --- 
+    - sequence-insert-overlap: 
+        inserts: 
+        - open: 2
+          close: 4
+          source: ins1
+        - open: 3
+          close: 5
+          source: ins2
+        source: seq
+
+    """
+
+  Scenario: Validating a scaffold with two sets of overlapping inserts
+    Given a file named "sequence.fna" with:
+      """
+      >seq
+      ATGGCGGCTGA
+      >ins1
+      ATGGCG
+      >ins2
+      ATGGCG
+      """
+    Given a file named "scaffold.yml" with:
+      """
+      ---
+        -
+          sequence:
+            source: seq
+            inserts:
+            -
+              open: 2
+              close: 4
+              source: ins1
+            -
+              open: 3
+              close: 5
+              source: ins2
+            -
+              open: 6
+              close: 8
+              source: ins1
+            -
+              open: 7
+              close: 9
+              source: ins2
+      """
+    When I call "scaffolder" with arguments "validate scaffold.yml sequence.fna"
+    Then the exit status should be 0
+    And the stdout should contain exactly:
+    """
+    --- 
+    - sequence-insert-overlap: 
+        inserts: 
+        - open: 2
+          close: 4
+          source: ins1
+        - open: 3
+          close: 5
+          source: ins2
+        source: seq
+    - sequence-insert-overlap: 
+        inserts: 
+        - open: 6
+          close: 8
+          source: ins1
+        - open: 7
+          close: 9
+          source: ins2
+        source: seq
+
+    """

data/lib/scaffolder/binary_helper.rb

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+require 'scaffolder/tool_index'
+
+module Scaffolder::BinaryHelper
+  include Scaffolder::ToolIndex
+
+  DEFAULT_TOOL = Scaffolder::Tool::Help
+
+  def select_tool(name)
+    tool_exists?(name) ? get_tool(name) : DEFAULT_TOOL
+  end
+
+  def remove_first_argument(settings)
+    name = settings.rest.shift
+  end
+
+  def determine_tool(settings)
+    name = remove_first_argument(settings)
+
+    tool_class = select_tool(name)
+
+    if name.nil?
+      settings[:empty_args] = true
+    elsif not tool_exists?(name)
+      settings[:unknown_tool] = name
+    end
+
+    [tool_class,settings]
+  end
+
+end