genomer 0.0.5
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- data/.document +5 -0
- data/.gitignore +45 -0
- data/Gemfile +2 -0
- data/LICENSE.txt +20 -0
- data/README.rdoc +23 -0
- data/Rakefile +23 -0
- data/bin/genomer +18 -0
- data/cucumber.yml +2 -0
- data/features/api/annotation_ids.feature +152 -0
- data/features/api/annotation_location.feature +269 -0
- data/features/api/scaffold.feature +38 -0
- data/features/cli/create.feature +19 -0
- data/features/cli/error.feature +17 -0
- data/features/cli/help.feature +48 -0
- data/features/cli/man.feature +71 -0
- data/features/cli/plugins.feature +34 -0
- data/features/step_definitions/genomer_steps.rb +10 -0
- data/features/support/env.rb +13 -0
- data/genomer-plugin-simple/genomer-plugin-simple.gemspec +18 -0
- data/genomer-plugin-simple/lib/genomer-plugin-simple.rb +19 -0
- data/genomer-plugin-simple/man/genomer-simple-subcommand.ronn +6 -0
- data/genomer-plugin-simple/man/genomer-simple.ronn +6 -0
- data/genomer.gemspec +39 -0
- data/lib/genomer.rb +6 -0
- data/lib/genomer/error.rb +4 -0
- data/lib/genomer/plugin.rb +126 -0
- data/lib/genomer/runtime.rb +101 -0
- data/lib/genomer/version.rb +3 -0
- data/man/genomer-init.1.ronn +20 -0
- data/spec/genomer/plugin_spec.rb +341 -0
- data/spec/genomer/runtime_spec.rb +262 -0
- data/spec/spec_helper.rb +45 -0
- metadata +290 -0
data/.document
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data/.gitignore
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tmp
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*.gem
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# rcov generated
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coverage
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# rdoc generated
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rdoc
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# yard generated
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doc
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.yardoc
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# bundler
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.bundle
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# jeweler generated
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pkg
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# Have editor/IDE/OS specific files you need to ignore? Consider using a global gitignore:
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#
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# * Create a file at ~/.gitignore
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# * Include files you want ignored
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# * Run: git config --global core.excludesfile ~/.gitignore
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#
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# After doing this, these files will be ignored in all your git projects,
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# saving you from having to 'pollute' every project you touch with them
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#
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# Not sure what to needs to be ignored for particular editors/OSes? Here's some ideas to get you started. (Remember, remove the leading # of the line)
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#
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# For MacOS:
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#
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#.DS_Store
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#
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# For TextMate
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#*.tmproj
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#tmtags
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#
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# For emacs:
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#*~
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#\#*
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#.\#*
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#
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# For vim:
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#*.swp
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data/Gemfile
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data/LICENSE.txt
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Copyright (c) 2010 Michael Barton
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Permission is hereby granted, free of charge, to any person obtaining
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a copy of this software and associated documentation files (the
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"Software"), to deal in the Software without restriction, including
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without limitation the rights to use, copy, modify, merge, publish,
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distribute, sublicense, and/or sell copies of the Software, and to
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permit persons to whom the Software is furnished to do so, subject to
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the following conditions:
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The above copyright notice and this permission notice shall be
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included in all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
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LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
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OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
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WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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data/README.rdoc
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== Synopsis
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Genomer is a plugin-based framework for genome finishing. Plugins are installed
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using the RubyGems package management system. Genome files are managed as a
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directory and updated at the command line using the `genomer` command.
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== Installing
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Ruby and RubyGems are required to use genomer and related plugins. Genomer is
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installed on the command line using:
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$ gem install genomer
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== Contact
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Genomer is developed by Michael Barton (www.michaelbarton.me.uk). The source
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code is available on github. Bug reports and feature requests should also be
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made there.
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== Copyright
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Genomer copyright (c) 2010 by Michael Barton. Scaffolder is licensed under the
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MIT license. See LICENSE.txt for further details.
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data/Rakefile
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require 'rubygems'
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require 'bundler'
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begin
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Bundler.setup(:default, :development)
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rescue Bundler::BundlerError => e
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$stderr.puts e.message
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$stderr.puts "Run `bundle install` to install missing gems"
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exit e.status_code
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end
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require 'rake/dsl_definition'
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require 'rspec/core'
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require 'rspec/core/rake_task'
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require 'cucumber/rake/task'
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Bundler::GemHelper.install_tasks
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RSpec::Core::RakeTask.new(:spec) do |spec|
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spec.pattern = FileList['spec/**/*_spec.rb']
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end
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Cucumber::Rake::Task.new(:features)
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task :default => :spec
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data/bin/genomer
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#!/usr/bin/env ruby
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$:.unshift File.join(File.dirname(__FILE__), '..', 'lib')
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require 'rubygems'
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require 'configliere'
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require 'genomer'
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require 'ronn'
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Settings.use :commandline
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Settings.resolve!
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begin
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STDOUT.puts Genomer::Runtime.new(Settings).execute!
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exit true
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rescue Genomer::Error => e
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STDERR.puts "Error. #{e.message}"
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exit false
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end
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data/cucumber.yml
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Feature: Changing annotation IDs
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In order to tailor annotation IDs to specific genomes
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A plugin developer can pass options to the #annotations method
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So that the annotation IDs are correspondingly changed
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@disable-bundler
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Scenario: Adding a prefix to annotation IDs
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Given I run the genomer command with the arguments "init project"
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And I cd to "project"
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And I append to "Gemfile" with:
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"""
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gem 'genomer', :path => '../../../'
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gem 'genomer-plugin-simple', :path => '../../../genomer-plugin-simple'
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"""
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And I append to "assembly/scaffold.yml" with:
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"""
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---
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-
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sequence:
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source: contig1
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"""
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And I append to "assembly/sequence.fna" with:
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"""
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>contig1
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ATGCATGC
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"""
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And I append to "assembly/annotations.gff" with:
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"""
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##gff-version 3
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contig1 . gene 1 4 . + 1 ID=gene1
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contig1 . gene 5 8 . + 1 ID=gene2
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"""
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When I run the genomer command with the arguments "simple annotations --prefix=pre_"
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Then the exit status should be 0
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And the output should contain:
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"""
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##gff-version 3
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scaffold . gene 1 4 . + 1 ID=pre_gene1
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scaffold . gene 5 8 . + 1 ID=pre_gene2
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"""
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@disable-bundler
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Scenario: Reset locus tag numbering from the sequence start
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Given I run the genomer command with the arguments "init project"
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And I cd to "project"
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And I append to "Gemfile" with:
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"""
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gem 'genomer', :path => '../../../'
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gem 'genomer-plugin-simple', :path => '../../../genomer-plugin-simple'
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"""
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And I append to "assembly/scaffold.yml" with:
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"""
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---
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-
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sequence:
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source: contig1
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"""
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And I append to "assembly/sequence.fna" with:
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"""
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>contig1
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ATGCATGC
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"""
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And I append to "assembly/annotations.gff" with:
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"""
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##gff-version 3
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contig1 . gene 1 4 . + 1 ID=gene1
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contig1 . gene 5 8 . + 1 ID=gene2
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"""
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When I run the genomer command with the arguments "simple annotations --reset_locus_numbering"
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Then the exit status should be 0
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And the output should contain:
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"""
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##gff-version 3
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scaffold . gene 1 4 . + 1 ID=000001
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scaffold . gene 5 8 . + 1 ID=000002
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"""
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@disable-bundler
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Scenario: Reset locus tag numbering with at a specific value
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Given I run the genomer command with the arguments "init project"
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And I cd to "project"
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And I append to "Gemfile" with:
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"""
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gem 'genomer', :path => '../../../'
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gem 'genomer-plugin-simple', :path => '../../../genomer-plugin-simple'
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"""
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And I append to "assembly/scaffold.yml" with:
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"""
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---
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-
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sequence:
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source: contig1
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"""
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And I append to "assembly/sequence.fna" with:
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"""
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>contig1
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ATGCATGC
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"""
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And I append to "assembly/annotations.gff" with:
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"""
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##gff-version 3
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contig1 . gene 1 4 . + 1 ID=gene1
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contig1 . gene 5 8 . + 1 ID=gene2
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"""
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When I run the genomer command with the arguments "simple annotations --reset_locus_numbering=10"
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Then the exit status should be 0
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And the output should contain:
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"""
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##gff-version 3
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scaffold . gene 1 4 . + 1 ID=000010
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scaffold . gene 5 8 . + 1 ID=000011
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"""
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@disable-bundler
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Scenario: Reseting locus tag numbering and adding a prefix
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Given I run the genomer command with the arguments "init project"
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And I cd to "project"
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And I append to "Gemfile" with:
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"""
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gem 'genomer', :path => '../../../'
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gem 'genomer-plugin-simple', :path => '../../../genomer-plugin-simple'
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"""
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And I append to "assembly/scaffold.yml" with:
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"""
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---
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-
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sequence:
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source: contig1
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"""
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And I append to "assembly/sequence.fna" with:
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"""
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>contig1
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ATGCATGC
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"""
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And I append to "assembly/annotations.gff" with:
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"""
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##gff-version 3
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contig1 . gene 1 4 . + 1 ID=gene1
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contig1 . gene 5 8 . + 1 ID=gene2
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"""
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When I run the genomer command with the arguments "simple annotations --reset_locus_numbering --prefix=pre_"
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Then the exit status should be 0
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And the output should contain:
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"""
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##gff-version 3
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scaffold . gene 1 4 . + 1 ID=pre_000001
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scaffold . gene 5 8 . + 1 ID=pre_000002
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"""
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Feature: Accessing scaffold annotations
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In order to access gff annotations in a genomer plugin
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A plugin developer can access annotations from the #annotations method
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So that these annotations are available for use
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@disable-bundler
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Scenario: Two annotations on a single contig
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Given I run the genomer command with the arguments "init project"
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And I cd to "project"
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And I append to "Gemfile" with:
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"""
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gem 'genomer', :path => '../../../'
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gem 'genomer-plugin-simple', :path => '../../../genomer-plugin-simple'
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"""
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And I append to "assembly/scaffold.yml" with:
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"""
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---
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-
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sequence:
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source: contig1
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"""
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And I append to "assembly/sequence.fna" with:
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"""
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>contig1
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ATGCATGC
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"""
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And I append to "assembly/annotations.gff" with:
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"""
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##gff-version 3
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contig1 . gene 1 3 . + 1 .
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contig1 . gene 5 7 . + 1 .
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"""
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When I run the genomer command with the arguments "simple annotations"
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Then the exit status should be 0
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And the output should contain:
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"""
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##gff-version 3
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scaffold . gene 1 3 . + 1 .
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scaffold . gene 5 7 . + 1 .
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"""
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@disable-bundler
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Scenario: Two annotations on a two contigs
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Given I run the genomer command with the arguments "init project"
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And I cd to "project"
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And I append to "Gemfile" with:
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"""
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gem 'genomer', :path => '../../../'
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gem 'genomer-plugin-simple', :path => '../../../genomer-plugin-simple'
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"""
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And I append to "assembly/scaffold.yml" with:
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"""
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---
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-
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sequence:
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source: contig1
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-
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sequence:
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source: contig2
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"""
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And I append to "assembly/sequence.fna" with:
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"""
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>contig1
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ATGCATGC
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>contig2
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ATGCATGC
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"""
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And I append to "assembly/annotations.gff" with:
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"""
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##gff-version 3
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contig1 . gene 1 3 . + 1 .
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contig2 . gene 5 7 . + 1 .
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"""
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When I run the genomer command with the arguments "simple annotations"
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Then the exit status should be 0
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And the output should contain:
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"""
|
80
|
+
##gff-version 3
|
81
|
+
scaffold . gene 1 3 . + 1 .
|
82
|
+
scaffold . gene 13 15 . + 1 .
|
83
|
+
"""
|
84
|
+
|
85
|
+
@disable-bundler
|
86
|
+
Scenario: Two annotations on a single contig with an unused annotation
|
87
|
+
Given I run the genomer command with the arguments "init project"
|
88
|
+
And I cd to "project"
|
89
|
+
And I append to "Gemfile" with:
|
90
|
+
"""
|
91
|
+
gem 'genomer', :path => '../../../'
|
92
|
+
gem 'genomer-plugin-simple', :path => '../../../genomer-plugin-simple'
|
93
|
+
"""
|
94
|
+
And I append to "assembly/scaffold.yml" with:
|
95
|
+
"""
|
96
|
+
---
|
97
|
+
-
|
98
|
+
sequence:
|
99
|
+
source: contig1
|
100
|
+
|
101
|
+
"""
|
102
|
+
And I append to "assembly/sequence.fna" with:
|
103
|
+
"""
|
104
|
+
>contig1
|
105
|
+
ATGCATGC
|
106
|
+
"""
|
107
|
+
And I append to "assembly/annotations.gff" with:
|
108
|
+
"""
|
109
|
+
##gff-version 3
|
110
|
+
contig2 . gene 5 7 . + 1 .
|
111
|
+
contig1 . gene 1 3 . + 1 .
|
112
|
+
contig1 . gene 5 7 . + 1 .
|
113
|
+
"""
|
114
|
+
When I run the genomer command with the arguments "simple annotations"
|
115
|
+
Then the exit status should be 0
|
116
|
+
And the output should contain:
|
117
|
+
"""
|
118
|
+
##gff-version 3
|
119
|
+
scaffold . gene 1 3 . + 1 .
|
120
|
+
scaffold . gene 5 7 . + 1 .
|
121
|
+
"""
|
122
|
+
|
123
|
+
@disable-bundler
|
124
|
+
Scenario: Three unordered annotations on a single contig
|
125
|
+
Given I run the genomer command with the arguments "init project"
|
126
|
+
And I cd to "project"
|
127
|
+
And I append to "Gemfile" with:
|
128
|
+
"""
|
129
|
+
gem 'genomer', :path => '../../../'
|
130
|
+
gem 'genomer-plugin-simple', :path => '../../../genomer-plugin-simple'
|
131
|
+
"""
|
132
|
+
And I append to "assembly/scaffold.yml" with:
|
133
|
+
"""
|
134
|
+
---
|
135
|
+
-
|
136
|
+
sequence:
|
137
|
+
source: contig1
|
138
|
+
|
139
|
+
"""
|
140
|
+
And I append to "assembly/sequence.fna" with:
|
141
|
+
"""
|
142
|
+
>contig1
|
143
|
+
ATGCATGCATGC
|
144
|
+
"""
|
145
|
+
And I append to "assembly/annotations.gff" with:
|
146
|
+
"""
|
147
|
+
##gff-version 3
|
148
|
+
contig1 . gene 9 11 . + 1 .
|
149
|
+
contig1 . gene 1 3 . + 1 .
|
150
|
+
contig1 . gene 5 7 . + 1 .
|
151
|
+
"""
|
152
|
+
When I run the genomer command with the arguments "simple annotations"
|
153
|
+
Then the exit status should be 0
|
154
|
+
And the output should contain:
|
155
|
+
"""
|
156
|
+
##gff-version 3
|
157
|
+
scaffold . gene 1 3 . + 1 .
|
158
|
+
scaffold . gene 5 7 . + 1 .
|
159
|
+
scaffold . gene 9 11 . + 1 .
|
160
|
+
"""
|
161
|
+
|
162
|
+
@disable-bundler
|
163
|
+
Scenario: Four unordered annotations on a two contigs
|
164
|
+
Given I run the genomer command with the arguments "init project"
|
165
|
+
And I cd to "project"
|
166
|
+
And I append to "Gemfile" with:
|
167
|
+
"""
|
168
|
+
gem 'genomer', :path => '../../../'
|
169
|
+
gem 'genomer-plugin-simple', :path => '../../../genomer-plugin-simple'
|
170
|
+
"""
|
171
|
+
And I append to "assembly/scaffold.yml" with:
|
172
|
+
"""
|
173
|
+
---
|
174
|
+
-
|
175
|
+
sequence:
|
176
|
+
source: contig1
|
177
|
+
-
|
178
|
+
sequence:
|
179
|
+
source: contig2
|
180
|
+
|
181
|
+
"""
|
182
|
+
And I append to "assembly/sequence.fna" with:
|
183
|
+
"""
|
184
|
+
>contig1
|
185
|
+
ATGCATGC
|
186
|
+
>contig2
|
187
|
+
ATGCATGC
|
188
|
+
"""
|
189
|
+
And I append to "assembly/annotations.gff" with:
|
190
|
+
"""
|
191
|
+
##gff-version 3
|
192
|
+
contig2 . gene 5 7 . + 1 .
|
193
|
+
contig2 . gene 1 3 . + 1 .
|
194
|
+
contig1 . gene 1 3 . + 1 .
|
195
|
+
contig1 . gene 5 7 . + 1 .
|
196
|
+
"""
|
197
|
+
When I run the genomer command with the arguments "simple annotations"
|
198
|
+
Then the exit status should be 0
|
199
|
+
And the output should contain:
|
200
|
+
"""
|
201
|
+
##gff-version 3
|
202
|
+
scaffold . gene 1 3 . + 1 .
|
203
|
+
scaffold . gene 5 7 . + 1 .
|
204
|
+
scaffold . gene 9 11 . + 1 .
|
205
|
+
scaffold . gene 13 15 . + 1 .
|
206
|
+
|
207
|
+
"""
|
208
|
+
|
209
|
+
@disable-bundler
|
210
|
+
Scenario: Annotations on reversed and trimmed contigs with inserts
|
211
|
+
Given I run the genomer command with the arguments "init project"
|
212
|
+
And I cd to "project"
|
213
|
+
And I append to "Gemfile" with:
|
214
|
+
"""
|
215
|
+
gem 'genomer', :path => '../../../'
|
216
|
+
gem 'genomer-plugin-simple', :path => '../../../genomer-plugin-simple'
|
217
|
+
"""
|
218
|
+
And I append to "assembly/scaffold.yml" with:
|
219
|
+
"""
|
220
|
+
---
|
221
|
+
- sequence:
|
222
|
+
source: contig1
|
223
|
+
stop: 6
|
224
|
+
- sequence:
|
225
|
+
source: contig2
|
226
|
+
reverse: true
|
227
|
+
inserts:
|
228
|
+
-
|
229
|
+
source: insert1
|
230
|
+
open: 6
|
231
|
+
close: 7
|
232
|
+
- sequence:
|
233
|
+
source: contig3
|
234
|
+
start: 3
|
235
|
+
|
236
|
+
"""
|
237
|
+
And I append to "assembly/sequence.fna" with:
|
238
|
+
"""
|
239
|
+
> contig1
|
240
|
+
AAAAAGGG
|
241
|
+
> contig2
|
242
|
+
AAAAAGGGGGC
|
243
|
+
> contig3
|
244
|
+
AAAAAGGG
|
245
|
+
> insert1
|
246
|
+
TTT
|
247
|
+
"""
|
248
|
+
And I append to "assembly/annotations.gff" with:
|
249
|
+
"""
|
250
|
+
##gff-version 3
|
251
|
+
contig1 . gene 1 4 . + 1 ID=gene1
|
252
|
+
contig1 . gene 5 8 . + 1 ID=gene2
|
253
|
+
contig2 . gene 1 4 . + 1 ID=gene3
|
254
|
+
contig2 . gene 8 11 . + 1 ID=gene4
|
255
|
+
contig3 . gene 1 3 . + 1 ID=gene5
|
256
|
+
contig3 . gene 4 8 . + 1 ID=gene6
|
257
|
+
|
258
|
+
"""
|
259
|
+
When I run the genomer command with the arguments "simple annotations"
|
260
|
+
Then the exit status should be 0
|
261
|
+
And the output should contain:
|
262
|
+
"""
|
263
|
+
##gff-version 3
|
264
|
+
scaffold . gene 1 4 . + 1 ID=gene1
|
265
|
+
scaffold . gene 7 10 . - 1 ID=gene4
|
266
|
+
scaffold . gene 15 18 . - 1 ID=gene3
|
267
|
+
scaffold . gene 20 24 . + 1 ID=gene6
|
268
|
+
|
269
|
+
"""
|