genomer 0.0.5

data/.document

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+lib/**/*.rb
+bin/*
+- 
+features/**/*.feature
+LICENSE.txt

data/.gitignore

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+tmp
+*.gem
+
+# rcov generated
+coverage
+
+# rdoc generated
+rdoc
+
+# yard generated
+doc
+.yardoc
+
+# bundler
+.bundle
+
+# jeweler generated
+pkg
+
+# Have editor/IDE/OS specific files you need to ignore? Consider using a global gitignore: 
+#
+# * Create a file at ~/.gitignore
+# * Include files you want ignored
+# * Run: git config --global core.excludesfile ~/.gitignore
+#
+# After doing this, these files will be ignored in all your git projects,
+# saving you from having to 'pollute' every project you touch with them
+#
+# 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)
+#
+# For MacOS:
+#
+#.DS_Store
+#
+# For TextMate
+#*.tmproj
+#tmtags
+#
+# For emacs:
+#*~
+#\#*
+#.\#*
+#
+# For vim:
+#*.swp

data/Gemfile

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+source :rubygems
+gemspec

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
+
+Genomer is a plugin-based framework for genome finishing. Plugins are installed
+using the RubyGems package management system. Genome files are managed as a
+directory and updated at the command line using the `genomer` command.
+
+== Installing
+
+Ruby and RubyGems are required to use genomer and related plugins. Genomer is
+installed on the command line using:
+
+  $ gem install genomer
+
+== Contact
+
+Genomer is developed by Michael Barton (www.michaelbarton.me.uk). The source
+code is available on github. Bug reports and feature requests should also be
+made there.
+
+== Copyright
+
+Genomer copyright (c) 2010 by Michael Barton. Scaffolder is licensed under the
+MIT license. See LICENSE.txt for further details.

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/dsl_definition'
+require 'rspec/core'
+require 'rspec/core/rake_task'
+require 'cucumber/rake/task'
+
+Bundler::GemHelper.install_tasks
+
+RSpec::Core::RakeTask.new(:spec) do |spec|
+  spec.pattern = FileList['spec/**/*_spec.rb']
+end
+
+Cucumber::Rake::Task.new(:features)
+
+task :default => :spec

data/bin/genomer

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+#!/usr/bin/env ruby
+$:.unshift File.join(File.dirname(__FILE__), '..', 'lib')
+
+require 'rubygems'
+require 'configliere'
+require 'genomer'
+require 'ronn'
+
+Settings.use :commandline
+Settings.resolve!
+
+begin
+  STDOUT.puts Genomer::Runtime.new(Settings).execute!
+  exit true
+rescue Genomer::Error => e
+  STDERR.puts "Error. #{e.message}"
+  exit false
+end

data/cucumber.yml

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+---
+  default: --format progress --color

data/features/api/annotation_ids.feature

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+Feature: Changing annotation IDs
+  In order to tailor annotation IDs to specific genomes
+  A plugin developer can pass options to the #annotations method
+  So that the annotation IDs are correspondingly changed
+
+  @disable-bundler
+  Scenario: Adding a prefix to annotation IDs
+    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
+
+        """
+      And I append to "assembly/sequence.fna" with:
+        """
+        >contig1
+        ATGCATGC
+        """
+      And I append to "assembly/annotations.gff" with:
+        """
+        ##gff-version 3
+        contig1	.	gene	1	4	.	+	1	ID=gene1
+        contig1	.	gene	5	8	.	+	1	ID=gene2
+        """
+     When I run the genomer command with the arguments "simple annotations --prefix=pre_"
+     Then the exit status should be 0
+      And the output should contain:
+        """
+        ##gff-version 3
+        scaffold	.	gene	1	4	.	+	1	ID=pre_gene1
+        scaffold	.	gene	5	8	.	+	1	ID=pre_gene2
+        """
+
+  @disable-bundler
+  Scenario: Reset locus tag numbering from the sequence start
+    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
+
+        """
+      And I append to "assembly/sequence.fna" with:
+        """
+        >contig1
+        ATGCATGC
+        """
+      And I append to "assembly/annotations.gff" with:
+        """
+        ##gff-version 3
+        contig1	.	gene	1	4	.	+	1	ID=gene1
+        contig1	.	gene	5	8	.	+	1	ID=gene2
+        """
+     When I run the genomer command with the arguments "simple annotations --reset_locus_numbering"
+     Then the exit status should be 0
+      And the output should contain:
+        """
+        ##gff-version 3
+        scaffold	.	gene	1	4	.	+	1	ID=000001
+        scaffold	.	gene	5	8	.	+	1	ID=000002
+        """
+
+  @disable-bundler
+  Scenario: Reset locus tag numbering with at a specific value
+    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
+
+        """
+      And I append to "assembly/sequence.fna" with:
+        """
+        >contig1
+        ATGCATGC
+        """
+      And I append to "assembly/annotations.gff" with:
+        """
+        ##gff-version 3
+        contig1	.	gene	1	4	.	+	1	ID=gene1
+        contig1	.	gene	5	8	.	+	1	ID=gene2
+        """
+      When I run the genomer command with the arguments "simple annotations --reset_locus_numbering=10"
+     Then the exit status should be 0
+      And the output should contain:
+        """
+        ##gff-version 3
+        scaffold	.	gene	1	4	.	+	1	ID=000010
+        scaffold	.	gene	5	8	.	+	1	ID=000011
+        """
+
+  @disable-bundler
+  Scenario: Reseting locus tag numbering and adding a prefix
+    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
+
+        """
+      And I append to "assembly/sequence.fna" with:
+        """
+        >contig1
+        ATGCATGC
+        """
+      And I append to "assembly/annotations.gff" with:
+        """
+        ##gff-version 3
+        contig1	.	gene	1	4	.	+	1	ID=gene1
+        contig1	.	gene	5	8	.	+	1	ID=gene2
+        """
+      When I run the genomer command with the arguments "simple annotations --reset_locus_numbering --prefix=pre_"
+     Then the exit status should be 0
+      And the output should contain:
+        """
+        ##gff-version 3
+        scaffold	.	gene	1	4	.	+	1	ID=pre_000001
+        scaffold	.	gene	5	8	.	+	1	ID=pre_000002
+        """

data/features/api/annotation_location.feature

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+Feature: Accessing scaffold annotations
+  In order to access gff annotations in a genomer plugin
+  A plugin developer can access annotations from the #annotations method
+  So that these annotations are available for use
+
+  @disable-bundler
+  Scenario: Two annotations on a single contig
+    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
+
+        """
+      And I append to "assembly/sequence.fna" with:
+        """
+        >contig1
+        ATGCATGC
+        """
+      And I append to "assembly/annotations.gff" with:
+        """
+        ##gff-version 3
+        contig1	.	gene	1	3	.	+	1	.
+        contig1	.	gene	5	7	.	+	1	.
+        """
+     When I run the genomer command with the arguments "simple annotations"
+     Then the exit status should be 0
+      And the output should contain:
+        """
+        ##gff-version 3
+        scaffold	.	gene	1	3	.	+	1	.
+        scaffold	.	gene	5	7	.	+	1	.
+        """
+
+  @disable-bundler
+  Scenario: Two annotations on a two contigs
+    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
+        ATGCATGC
+        >contig2
+        ATGCATGC
+        """
+      And I append to "assembly/annotations.gff" with:
+        """
+        ##gff-version 3
+        contig1	.	gene	1	3	.	+	1	.
+        contig2	.	gene	5	7	.	+	1	.
+        """
+     When I run the genomer command with the arguments "simple annotations"
+     Then the exit status should be 0
+      And the output should contain:
+        """
+        ##gff-version 3
+        scaffold	.	gene	1	3	.	+	1	.
+        scaffold	.	gene	13	15	.	+	1	.
+        """
+
+  @disable-bundler
+  Scenario: Two annotations on a single contig with an unused annotation
+    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
+
+        """
+      And I append to "assembly/sequence.fna" with:
+        """
+        >contig1
+        ATGCATGC
+        """
+      And I append to "assembly/annotations.gff" with:
+        """
+        ##gff-version 3
+        contig2	.	gene	5	7	.	+	1	.
+        contig1	.	gene	1	3	.	+	1	.
+        contig1	.	gene	5	7	.	+	1	.
+        """
+     When I run the genomer command with the arguments "simple annotations"
+     Then the exit status should be 0
+      And the output should contain:
+        """
+        ##gff-version 3
+        scaffold	.	gene	1	3	.	+	1	.
+        scaffold	.	gene	5	7	.	+	1	.
+        """
+
+  @disable-bundler
+  Scenario: Three unordered annotations on a single contig
+    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
+
+        """
+      And I append to "assembly/sequence.fna" with:
+        """
+        >contig1
+        ATGCATGCATGC
+        """
+      And I append to "assembly/annotations.gff" with:
+        """
+        ##gff-version 3
+        contig1	.	gene	9	11	.	+	1	.
+        contig1	.	gene	1	3	.	+	1	.
+        contig1	.	gene	5	7	.	+	1	.
+        """
+     When I run the genomer command with the arguments "simple annotations"
+     Then the exit status should be 0
+      And the output should contain:
+        """
+        ##gff-version 3
+        scaffold	.	gene	1	3	.	+	1	.
+        scaffold	.	gene	5	7	.	+	1	.
+        scaffold	.	gene	9	11	.	+	1	.
+        """
+
+  @disable-bundler
+  Scenario: Four unordered annotations on a two contigs
+    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
+        ATGCATGC
+        >contig2
+        ATGCATGC
+        """
+      And I append to "assembly/annotations.gff" with:
+        """
+        ##gff-version 3
+        contig2	.	gene	5	7	.	+	1	.
+        contig2	.	gene	1	3	.	+	1	.
+        contig1	.	gene	1	3	.	+	1	.
+        contig1	.	gene	5	7	.	+	1	.
+        """
+     When I run the genomer command with the arguments "simple annotations"
+     Then the exit status should be 0
+      And the output should contain:
+        """
+        ##gff-version 3
+        scaffold	.	gene	1	3	.	+	1	.
+        scaffold	.	gene	5	7	.	+	1	.
+        scaffold	.	gene	9	11	.	+	1	.
+        scaffold	.	gene	13	15	.	+	1	.
+
+        """
+
+  @disable-bundler
+  Scenario: Annotations on reversed and trimmed contigs with inserts
+    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
+              stop: 6
+          - sequence:
+              source: contig2
+              reverse: true
+              inserts:
+              -
+                source: insert1
+                open: 6
+                close: 7
+          - sequence:
+              source: contig3
+              start: 3
+
+        """
+      And I append to "assembly/sequence.fna" with:
+        """
+        > contig1
+        AAAAAGGG
+        > contig2
+        AAAAAGGGGGC
+        > contig3
+        AAAAAGGG
+        > insert1
+        TTT
+        """
+      And I append to "assembly/annotations.gff" with:
+        """
+        ##gff-version 3
+        contig1	.	gene	1	4	.	+	1	ID=gene1
+        contig1	.	gene	5	8	.	+	1	ID=gene2
+        contig2	.	gene	1	4	.	+	1	ID=gene3
+        contig2	.	gene	8	11	.	+	1	ID=gene4
+        contig3	.	gene	1	3	.	+	1	ID=gene5
+        contig3	.	gene	4	8	.	+	1	ID=gene6
+
+        """
+     When I run the genomer command with the arguments "simple annotations"
+     Then the exit status should be 0
+      And the output should contain:
+        """
+        ##gff-version 3
+        scaffold	.	gene	1	4	.	+	1	ID=gene1
+        scaffold	.	gene	7	10	.	-	1	ID=gene4
+        scaffold	.	gene	15	18	.	-	1	ID=gene3
+        scaffold	.	gene	20	24	.	+	1	ID=gene6
+
+        """