genomer-plugin-view 0.0.2

data/.document

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

data/.gitignore

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+# rcov generated
+coverage
+
+# rdoc generated
+rdoc
+
+# yard generated
+doc
+.yardoc
+
+# bundler
+.bundle
+
+# jeweler generated
+pkg
+
+# ronn generated
+man/*.[1-9]
+man/*.[1-9].html
+
+# 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
+
+# For redcar:
+#.redcar
+
+# For rubinius:
+#*.rbc

data/Gemfile

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+source :rubygems
+gemspec

data/LICENSE.txt

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+Copyright (c) 2011 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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+= genomer-plugin-view
+
+Description goes here.
+
+== Contributing to genomer-plugin-view
+ 
+* Check out the latest master to make sure the feature hasn't been implemented or the bug hasn't been fixed yet
+* Check out the issue tracker to make sure someone already hasn't requested it and/or contributed it
+* Fork the project
+* Start a feature/bugfix branch
+* Commit and push until you are happy with your contribution
+* Make sure to add tests for it. This is important so I don't break it in a future version unintentionally.
+* Please try not to mess with the Rakefile, version, or history. If you want to have your own version, or is otherwise necessary, that is fine, but please isolate to its own commit so I can cherry-pick around it.
+
+== Copyright
+
+Copyright (c) 2011 Michael Barton. See LICENSE.txt for
+further details.
+

data/Rakefile

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+#!/usr/bin/env rake
+require "bundler/gem_tasks"
+require 'rspec/core/rake_task'
+
+RSpec::Core::RakeTask.new(:spec) do |spec|
+  spec.pattern = FileList['spec/**/*_spec.rb']
+end
+
+task :default => :spec

data/features/agp/generation.feature

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+Feature: Producing an agp view of a scaffold
+  In order to produce submit an incomplete scaffold
+  A user can use the "agp" command
+  to generate an agp file of the scaffold
+
+  @disable-bundler
+  Scenario: A single contig scaffold
+    Given I successfully run `genomer init project`
+      And I cd to "project"
+      And I write to "assembly/scaffold.yml" with:
+      """
+      ---
+      -
+        sequence:
+          source: "contig00001"
+      """
+      And I write to "assembly/sequence.fna" with:
+      """
+      >contig00001
+      ATGGC
+      """
+      And I append to "Gemfile" with:
+      """
+      gem 'genomer-plugin-view', :path => '../../../'
+      """
+     When I run `genomer view agp`
+     Then the exit status should be 0
+      And the output should contain:
+     """
+     ##agp-version	2.0
+     scaffold	1	5	1	W	contig00001	1	5	+
+     """
+
+  @disable-bundler
+  Scenario: A two contig scaffold
+    Given I successfully run `genomer init project`
+      And I cd to "project"
+      And I write to "assembly/scaffold.yml" with:
+      """
+      ---
+      -
+        sequence:
+          source: "contig00001"
+      -
+        sequence:
+          source: "contig00002"
+      """
+      And I write to "assembly/sequence.fna" with:
+      """
+      >contig00001
+      ATGGC
+      >contig00002
+      ATGGC
+      """
+      And I append to "Gemfile" with:
+      """
+      gem 'genomer-plugin-view', :path => '../../../'
+      """
+     When I run `genomer view agp`
+     Then the exit status should be 0
+      And the output should contain:
+     """
+     ##agp-version	2.0
+     scaffold	1	5	1	W	contig00001	1	5	+
+     scaffold	6	10	2	W	contig00002	1	5	+
+     """
+
+  @disable-bundler
+  Scenario: A single contig scaffold with a gap
+    Given I successfully run `genomer init project`
+      And I cd to "project"
+      And I write to "assembly/scaffold.yml" with:
+      """
+      ---
+      -
+        sequence:
+          source: "contig00001"
+      """
+      And I write to "assembly/sequence.fna" with:
+      """
+      >contig00001
+      ATGNNNGCG
+      """
+      And I append to "Gemfile" with:
+      """
+      gem 'genomer-plugin-view', :path => '../../../'
+      """
+     When I run `genomer view agp`
+     Then the exit status should be 0
+      And the output should contain:
+     """
+     ##agp-version	2.0
+     scaffold	1	3	1	W	contig00001	1	3	+
+     scaffold	4	6	2	N	3	scaffold	yes	internal
+     scaffold	7	9	3	W	contig00002	1	3	+
+     """
+
+  @disable-bundler
+  Scenario: Two contigs scaffold containing gaps
+    Given I successfully run `genomer init project`
+      And I cd to "project"
+      And I write to "assembly/scaffold.yml" with:
+      """
+      ---
+      -
+        sequence:
+          source: "contig00001"
+      -
+        sequence:
+          source: "contig00002"
+      """
+      And I write to "assembly/sequence.fna" with:
+      """
+      >contig00001
+      ATGNNNGCG
+      >contig00002
+      ANG
+      """
+      And I append to "Gemfile" with:
+      """
+      gem 'genomer-plugin-view', :path => '../../../'
+      """
+     When I run `genomer view agp`
+     Then the exit status should be 0
+      And the output should contain:
+     """
+     ##agp-version	2.0
+     scaffold	1	3	1	W	contig00001	1	3	+
+     scaffold	4	6	2	N	3	scaffold	yes	internal
+     scaffold	7	9	3	W	contig00002	1	3	+
+     scaffold	10	10	4	W	contig00003	1	1	+
+     scaffold	11	11	5	N	1	scaffold	yes	internal
+     scaffold	12	12	6	W	contig00004	1	1	+
+     """
+
+  @disable-bundler
+  Scenario: Two contigs separated by an unresolved region
+    Given I successfully run `genomer init project`
+      And I cd to "project"
+      And I write to "assembly/scaffold.yml" with:
+      """
+      ---
+      -
+        sequence:
+          source: "contig00001"
+      -
+        unresolved:
+          length: 5
+      -
+        sequence:
+          source: "contig00002"
+      """
+      And I write to "assembly/sequence.fna" with:
+      """
+      >contig00001
+      ATGAT
+      >contig00002
+      ATGAT
+      """
+      And I append to "Gemfile" with:
+      """
+      gem 'genomer-plugin-view', :path => '../../../'
+      """
+     When I run `genomer view agp`
+     Then the exit status should be 0
+      And the output should contain:
+     """
+     ##agp-version	2.0
+     scaffold	1	5	1	W	contig00001	1	5	+
+     scaffold	6	10	2	N	5	scaffold	yes	specified
+     scaffold	11	15	3	W	contig00002	1	5	+
+     """
+
+  @disable-bundler
+  Scenario: Two contigs separated by an unresolved region
+    Given I successfully run `genomer init project`
+      And I cd to "project"
+      And I write to "assembly/scaffold.yml" with:
+      """
+      ---
+      -
+        sequence:
+          source: "contig00001"
+      -
+        unresolved:
+          length: 5
+      -
+        sequence:
+          source: "contig00002"
+      """
+      And I write to "assembly/sequence.fna" with:
+      """
+      >contig00001
+      ATGATNNNNN
+      >contig00002
+      ATGATNNNNN
+      """
+      And I append to "Gemfile" with:
+      """
+      gem 'genomer-plugin-view', :path => '../../../'
+      """
+     When I run `genomer view agp`
+     Then the exit status should be 0
+      And the output should contain:
+     """
+     ##agp-version	2.0
+     scaffold	1	5	1	W	contig00001	1	5	+
+     scaffold	6	10	2	N	5	scaffold	yes	internal
+     scaffold	11	15	3	N	5	scaffold	yes	specified
+     scaffold	16	20	4	W	contig00002	1	5	+
+     scaffold	21	25	5	N	5	scaffold	yes	internal
+     """
+
+  @disable-bundler
+  Scenario: A single contig scaffold with a gap filled with an insert
+    Given I successfully run `genomer init project`
+      And I cd to "project"
+      And I write to "assembly/scaffold.yml" with:
+      """
+      ---
+      -
+        sequence:
+          source: "contig00001"
+          inserts:
+          -
+            source: "insert00001"
+            open: 4
+            close: 6
+      """
+      And I write to "assembly/sequence.fna" with:
+      """
+      >contig00001
+      ATGNNNGCG
+      >insert00001
+      TTT
+      """
+      And I append to "Gemfile" with:
+      """
+      gem 'genomer-plugin-view', :path => '../../../'
+      """
+     When I run `genomer view agp`
+     Then the exit status should be 0
+      And the output should contain:
+     """
+     ##agp-version	2.0
+     scaffold	1	9	1	W	contig00001	1	9	+
+     """
+
+  @disable-bundler
+  Scenario: A single contig scaffold with a gap partially filled with an insert
+    Given I successfully run `genomer init project`
+      And I cd to "project"
+      And I write to "assembly/scaffold.yml" with:
+      """
+      ---
+      -
+        sequence:
+          source: "contig00001"
+          inserts:
+          -
+            source: "insert00001"
+            open: 4
+            close: 5
+      """
+      And I write to "assembly/sequence.fna" with:
+      """
+      >contig00001
+      ATGNNNGCG
+      >insert00001
+      TTT
+      """
+      And I append to "Gemfile" with:
+      """
+      gem 'genomer-plugin-view', :path => '../../../'
+      """
+     When I run `genomer view agp`
+     Then the exit status should be 0
+      And the output should contain:
+     """
+     ##agp-version	2.0
+     scaffold	1	6	1	W	contig00001	1	6	+
+     scaffold	7	7	2	N	1	scaffold	yes	internal
+     scaffold	8	10	3	W	contig00002	1	3	+
+     """
+

data/features/fasta/contigs.feature

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+Feature: Producing a fasta view of scaffold contigs
+  In order to produce fasta output of the scaffold contigs
+  A user can use the "view" command with the "--contigs" flag
+  to generate the contigs in fasta format
+
+  @disable-bundler
+  Scenario: A single contig scaffold
+    Given I successfully run `genomer init project`
+      And I cd to "project"
+      And I write to "assembly/scaffold.yml" with:
+      """
+      ---
+      -
+        sequence:
+          source: "contig00001"
+      """
+      And I write to "assembly/sequence.fna" with:
+      """
+      >contig00001
+      ATGGC
+      """
+      And I append to "Gemfile" with:
+      """
+      gem 'genomer-plugin-view', :path => '../../../'
+      """
+     When I run `genomer view fasta  --contigs`
+     Then the exit status should be 0
+      And the output should contain:
+     """
+     >contig00001
+     ATGGC
+     """
+
+  @disable-bundler
+  Scenario: A two contig scaffold generating a single sequence
+    Given I successfully run `genomer init project`
+      And I cd to "project"
+      And I write to "assembly/scaffold.yml" with:
+      """
+      ---
+      -
+        sequence:
+          source: "contig00001"
+      -
+        sequence:
+          source: "contig00002"
+      """
+      And I write to "assembly/sequence.fna" with:
+      """
+      >contig00001
+      ATGGC
+      >contig00002
+      ATGGC
+      """
+      And I append to "Gemfile" with:
+      """
+      gem 'genomer-plugin-view', :path => '../../../'
+      """
+     When I run `genomer view fasta --contigs`
+     Then the exit status should be 0
+      And the output should contain:
+     """
+     >contig00001
+     ATGGCATGGC
+     """
+
+  @disable-bundler
+  Scenario: A single contig scaffold containing a sequence of Ns
+    Given I successfully run `genomer init project`
+      And I cd to "project"
+      And I write to "assembly/scaffold.yml" with:
+      """
+      ---
+      -
+        sequence:
+          source: "contig00001"
+      """
+      And I write to "assembly/sequence.fna" with:
+      """
+      >contig00001
+      ATGGCNNNNATGGC
+      """
+      And I append to "Gemfile" with:
+      """
+      gem 'genomer-plugin-view', :path => '../../../'
+      """
+     When I run `genomer view fasta --contigs`
+     Then the exit status should be 0
+      And the output should contain:
+     """
+     >contig00001
+     ATGGC
+     >contig00002
+     ATGGC
+     """
+
+  @disable-bundler
+  Scenario: A two contig scaffold with an unresolved region
+    Given I successfully run `genomer init project`
+      And I cd to "project"
+      And I write to "assembly/scaffold.yml" with:
+      """
+      ---
+      -
+        sequence:
+          source: "A"
+      -
+        unresolved:
+          length: 10
+      -
+        sequence:
+          source: "B"
+      """
+      And I write to "assembly/sequence.fna" with:
+      """
+      >A
+      AAAAA
+      >B
+      CCCCC
+      """
+      And I append to "Gemfile" with:
+      """
+      gem 'genomer-plugin-view', :path => '../../../'
+      """
+     When I run `genomer view fasta --contigs`
+     Then the exit status should be 0
+      And the output should contain:
+     """
+     >contig00001
+     AAAAA
+     >contig00002
+     CCCCC
+     """
+
+  @disable-bundler
+  Scenario: A two contig scaffold with an unresolved region and gapped contig
+    Given I successfully run `genomer init project`
+      And I cd to "project"
+      And I write to "assembly/scaffold.yml" with:
+      """
+      ---
+      -
+        sequence:
+          source: "A"
+      -
+        unresolved:
+          length: 10
+      -
+        sequence:
+          source: "B"
+      """
+      And I write to "assembly/sequence.fna" with:
+      """
+      >A
+      AAAAA
+      >B
+      CCCNNNNTTT
+      """
+      And I append to "Gemfile" with:
+      """
+      gem 'genomer-plugin-view', :path => '../../../'
+      """
+     When I run `genomer view fasta --contigs`
+     Then the exit status should be 0
+      And the output should contain:
+     """
+     >contig00001
+     AAAAA
+     >contig00002
+     CCC
+     >contig00003
+     TTT
+     """