genomer 0.0.6 → 0.0.7

data/features/api/annotation_ids.feature

@@ -7,12 +7,12 @@ Feature: Changing annotation IDs
   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:
+      And I overwrite "Gemfile" with:
         """
         gem 'genomer',               :path => '../../../'
         gem 'genomer-plugin-simple', :path => '../../../genomer-plugin-simple'
         """
-      And I append to "assembly/scaffold.yml" with:
+      And I overwrite "assembly/scaffold.yml" with:
         """
         ---
         -
@@ -20,12 +20,12 @@ Feature: Changing annotation IDs
             source: contig1
 
         """
-      And I append to "assembly/sequence.fna" with:
+      And I overwrite "assembly/sequence.fna" with:
         """
         >contig1
         ATGCATGC
         """
-      And I append to "assembly/annotations.gff" with:
+      And I overwrite "assembly/annotations.gff" with:
         """
         ##gff-version 3
         contig1	.	gene	1	4	.	+	1	ID=gene1
@@ -44,12 +44,12 @@ Feature: Changing annotation IDs
   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:
+      And I overwrite "Gemfile" with:
         """
         gem 'genomer',               :path => '../../../'
         gem 'genomer-plugin-simple', :path => '../../../genomer-plugin-simple'
         """
-      And I append to "assembly/scaffold.yml" with:
+      And I overwrite "assembly/scaffold.yml" with:
         """
         ---
         -
@@ -57,12 +57,12 @@ Feature: Changing annotation IDs
             source: contig1
 
         """
-      And I append to "assembly/sequence.fna" with:
+      And I overwrite "assembly/sequence.fna" with:
         """
         >contig1
         ATGCATGC
         """
-      And I append to "assembly/annotations.gff" with:
+      And I overwrite "assembly/annotations.gff" with:
         """
         ##gff-version 3
         contig1	.	gene	1	4	.	+	1	ID=gene1
@@ -81,12 +81,12 @@ Feature: Changing annotation IDs
   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:
+      And I overwrite "Gemfile" with:
         """
         gem 'genomer',               :path => '../../../'
         gem 'genomer-plugin-simple', :path => '../../../genomer-plugin-simple'
         """
-      And I append to "assembly/scaffold.yml" with:
+      And I overwrite "assembly/scaffold.yml" with:
         """
         ---
         -
@@ -94,12 +94,12 @@ Feature: Changing annotation IDs
             source: contig1
 
         """
-      And I append to "assembly/sequence.fna" with:
+      And I overwrite "assembly/sequence.fna" with:
         """
         >contig1
         ATGCATGC
         """
-      And I append to "assembly/annotations.gff" with:
+      And I overwrite "assembly/annotations.gff" with:
         """
         ##gff-version 3
         contig1	.	gene	1	4	.	+	1	ID=gene1
@@ -118,12 +118,12 @@ Feature: Changing annotation IDs
   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:
+      And I overwrite "Gemfile" with:
         """
         gem 'genomer',               :path => '../../../'
         gem 'genomer-plugin-simple', :path => '../../../genomer-plugin-simple'
         """
-      And I append to "assembly/scaffold.yml" with:
+      And I overwrite "assembly/scaffold.yml" with:
         """
         ---
         -
@@ -131,12 +131,12 @@ Feature: Changing annotation IDs
             source: contig1
 
         """
-      And I append to "assembly/sequence.fna" with:
+      And I overwrite "assembly/sequence.fna" with:
         """
         >contig1
         ATGCATGC
         """
-      And I append to "assembly/annotations.gff" with:
+      And I overwrite "assembly/annotations.gff" with:
         """
         ##gff-version 3
         contig1	.	gene	1	4	.	+	1	ID=gene1

data/features/api/annotation_location.feature

@@ -7,12 +7,12 @@ Feature: Accessing scaffold annotations
   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:
+      And I overwrite "Gemfile" with:
         """
         gem 'genomer',               :path => '../../../'
         gem 'genomer-plugin-simple', :path => '../../../genomer-plugin-simple'
         """
-      And I append to "assembly/scaffold.yml" with:
+      And I overwrite "assembly/scaffold.yml" with:
         """
         ---
         -
@@ -20,12 +20,12 @@ Feature: Accessing scaffold annotations
             source: contig1
 
         """
-      And I append to "assembly/sequence.fna" with:
+      And I overwrite "assembly/sequence.fna" with:
         """
         >contig1
         ATGCATGC
         """
-      And I append to "assembly/annotations.gff" with:
+      And I overwrite "assembly/annotations.gff" with:
         """
         ##gff-version 3
         contig1	.	gene	1	3	.	+	1	.
@@ -44,12 +44,12 @@ Feature: Accessing scaffold annotations
   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:
+      And I overwrite "Gemfile" with:
         """
         gem 'genomer',               :path => '../../../'
         gem 'genomer-plugin-simple', :path => '../../../genomer-plugin-simple'
         """
-      And I append to "assembly/scaffold.yml" with:
+      And I overwrite "assembly/scaffold.yml" with:
         """
         ---
         -
@@ -60,14 +60,14 @@ Feature: Accessing scaffold annotations
             source: contig2
 
         """
-      And I append to "assembly/sequence.fna" with:
+      And I overwrite "assembly/sequence.fna" with:
         """
         >contig1
         ATGCATGC
         >contig2
         ATGCATGC
         """
-      And I append to "assembly/annotations.gff" with:
+      And I overwrite "assembly/annotations.gff" with:
         """
         ##gff-version 3
         contig1	.	gene	1	3	.	+	1	.
@@ -86,12 +86,12 @@ Feature: Accessing scaffold annotations
   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:
+      And I overwrite "Gemfile" with:
         """
         gem 'genomer',               :path => '../../../'
         gem 'genomer-plugin-simple', :path => '../../../genomer-plugin-simple'
         """
-      And I append to "assembly/scaffold.yml" with:
+      And I overwrite "assembly/scaffold.yml" with:
         """
         ---
         -
@@ -99,12 +99,12 @@ Feature: Accessing scaffold annotations
             source: contig1
 
         """
-      And I append to "assembly/sequence.fna" with:
+      And I overwrite "assembly/sequence.fna" with:
         """
         >contig1
         ATGCATGC
         """
-      And I append to "assembly/annotations.gff" with:
+      And I overwrite "assembly/annotations.gff" with:
         """
         ##gff-version 3
         contig2	.	gene	5	7	.	+	1	.
@@ -124,12 +124,12 @@ Feature: Accessing scaffold annotations
   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:
+      And I overwrite "Gemfile" with:
         """
         gem 'genomer',               :path => '../../../'
         gem 'genomer-plugin-simple', :path => '../../../genomer-plugin-simple'
         """
-      And I append to "assembly/scaffold.yml" with:
+      And I overwrite "assembly/scaffold.yml" with:
         """
         ---
         -
@@ -137,12 +137,12 @@ Feature: Accessing scaffold annotations
             source: contig1
 
         """
-      And I append to "assembly/sequence.fna" with:
+      And I overwrite "assembly/sequence.fna" with:
         """
         >contig1
         ATGCATGCATGC
         """
-      And I append to "assembly/annotations.gff" with:
+      And I overwrite "assembly/annotations.gff" with:
         """
         ##gff-version 3
         contig1	.	gene	9	11	.	+	1	.
@@ -163,12 +163,12 @@ Feature: Accessing scaffold annotations
   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:
+      And I overwrite "Gemfile" with:
         """
         gem 'genomer',               :path => '../../../'
         gem 'genomer-plugin-simple', :path => '../../../genomer-plugin-simple'
         """
-      And I append to "assembly/scaffold.yml" with:
+      And I overwrite "assembly/scaffold.yml" with:
         """
         ---
         -
@@ -179,14 +179,14 @@ Feature: Accessing scaffold annotations
             source: contig2
 
         """
-      And I append to "assembly/sequence.fna" with:
+      And I overwrite "assembly/sequence.fna" with:
         """
         >contig1
         ATGCATGC
         >contig2
         ATGCATGC
         """
-      And I append to "assembly/annotations.gff" with:
+      And I overwrite "assembly/annotations.gff" with:
         """
         ##gff-version 3
         contig2	.	gene	5	7	.	+	1	.
@@ -210,12 +210,12 @@ Feature: Accessing scaffold annotations
   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:
+      And I overwrite "Gemfile" with:
         """
         gem 'genomer',               :path => '../../../'
         gem 'genomer-plugin-simple', :path => '../../../genomer-plugin-simple'
         """
-      And I append to "assembly/scaffold.yml" with:
+      And I overwrite "assembly/scaffold.yml" with:
         """
         ---
           - sequence:
@@ -234,7 +234,7 @@ Feature: Accessing scaffold annotations
               start: 3
 
         """
-      And I append to "assembly/sequence.fna" with:
+      And I overwrite "assembly/sequence.fna" with:
         """
         > contig1
         AAAAAGGG
@@ -245,7 +245,7 @@ Feature: Accessing scaffold annotations
         > insert1
         TTT
         """
-      And I append to "assembly/annotations.gff" with:
+      And I overwrite "assembly/annotations.gff" with:
         """
         ##gff-version 3
         contig1	.	gene	1	4	.	+	1	ID=gene1

data/features/cli/error.feature

@@ -6,7 +6,6 @@ Feature: Reporting genomer errors
   Scenario: Calling a non-specified genomer plugin
     Given I run the genomer command with the arguments "init project"
       And I cd to "project"
-      And I append to "Gemfile" with ""
      When I run the genomer command with the arguments "simple"
      Then the exit status should be 1
       And the output should contain:

data/features/cli/help.feature

@@ -35,7 +35,7 @@ Feature: Listing available commands
   Scenario: Running help with a single genomer plugins specified
     Given I run the genomer command with the arguments "init project"
       And I cd to "project"
-      And I append to "Gemfile" with:
+      And I overwrite "Gemfile" with:
       """
       gem 'genomer-plugin-simple', :path => '../../../genomer-plugin-simple'
       """

data/features/cli/init.feature

@@ -0,0 +1,69 @@
+Feature: Creating a new genomer project
+  In order to build a genome
+  A user can create a new genomer project
+  So that they can use the genomer commands and organise their data
+
+  Scenario: Creating a new project
+    When I run the genomer command with the arguments "init project"
+    Then the exit status should be 0
+    And a directory named "project" should exist
+    And a directory named "project/assembly" should exist
+    And a file named "project/assembly/scaffold.yml" should exist
+    And the file "project/assembly/scaffold.yml" should contain exactly:
+    """
+    # Specify your genome scaffold in YAML format here. Reference nucleotide
+    # sequences in the 'sequences.fna' file using the first space delimited
+    # word of each fasta header.
+    #
+    # Go to http://next.gs/getting-started/ to start writing genome scaffold
+    # files.
+    #
+    # A simple one contig example is also provided below. Delete this as you
+    # start writing your own scaffold.
+    ---
+      -
+        sequence:
+          source: "contig1"
+
+    """
+    And a file named "project/assembly/sequence.fna" should exist
+    And the file "project/assembly/sequence.fna" should contain exactly:
+    """
+    ; Add your assembled contigs and scaffolds sequences to this file.
+    ; These sequences can be referenced in the 'scaffold.yml' file
+    ; using the first space delimited word in each fasta header.
+    > contig1
+    ATGC
+
+    """
+    And a file named "project/assembly/annotations.gff" should exist
+    And the file "project/assembly/annotations.gff" should contain exactly:
+    """
+    ##gff-version   3
+    ## Add your gff3 formatted annotations to this file
+
+    """
+    And a file named "project/Gemfile" should exist
+    And the file "project/Gemfile" should contain exactly:
+    """
+    source :rubygems
+
+    gem 'genomer',    '~> 0.0.0'
+
+    """
+
+  @disable-bundler
+  Scenario: Using the files generated in a new project
+    Given I run the genomer command with the arguments "init project"
+      And I cd to "project"
+      And I overwrite "Gemfile" with:
+      """
+      gem 'genomer',               :path => '../../../'
+      gem 'genomer-plugin-simple', :path => '../../../genomer-plugin-simple'
+      """
+     When I run the genomer command with the arguments "simple describe"
+     Then the exit status should be 0
+      And the output should contain:
+     """
+     The scaffold contains 1 entries
+     """

data/features/cli/man.feature

@@ -17,7 +17,7 @@ Feature: Showing man pages for available commands
   Scenario: Getting the man page for a plugin
     Given I run the genomer command with the arguments "init project"
       And I cd to "project"
-      And I append to "Gemfile" with:
+      And I overwrite "Gemfile" with:
       """
       gem 'genomer-plugin-simple', :path => '../../../genomer-plugin-simple'
       """
@@ -29,7 +29,7 @@ Feature: Showing man pages for available commands
   Scenario: Getting the man page for a plugin subcommand
     Given I run the genomer command with the arguments "init project"
       And I cd to "project"
-      And I append to "Gemfile" with:
+      And I overwrite "Gemfile" with:
       """
       gem 'genomer-plugin-simple', :path => '../../../genomer-plugin-simple'
       """
@@ -41,7 +41,7 @@ Feature: Showing man pages for available commands
   Scenario: Trying to get a man page for an unknown plugin
     Given I run the genomer command with the arguments "init project"
       And I cd to "project"
-      And I append to "Gemfile" with:
+      And I overwrite "Gemfile" with:
       """
       gem 'genomer-plugin-simple', :path => '../../../genomer-plugin-simple'
       """
@@ -58,7 +58,7 @@ Feature: Showing man pages for available commands
   Scenario: Trying to get a man page for an unknown subcommand
     Given I run the genomer command with the arguments "init project"
       And I cd to "project"
-      And I append to "Gemfile" with:
+      And I overwrite "Gemfile" with:
       """
       gem 'genomer-plugin-simple', :path => '../../../genomer-plugin-simple'
       """

data/features/cli/plugins.feature

@@ -7,7 +7,7 @@ Feature: Calling genomer plugins in a genomer project
   Scenario: Calling a genomer plugin with no command
     Given I run the genomer command with the arguments "init project"
       And I cd to "project"
-      And I append to "Gemfile" with:
+      And I overwrite "Gemfile" with:
       """
       gem 'genomer-plugin-simple', :path => '../../../genomer-plugin-simple'
       """
@@ -22,7 +22,7 @@ Feature: Calling genomer plugins in a genomer project
   Scenario: Calling a genomer plugin with a command
     Given I run the genomer command with the arguments "init project"
       And I cd to "project"
-      And I append to "Gemfile" with:
+      And I overwrite "Gemfile" with:
       """
       gem 'genomer-plugin-simple', :path => '../../../genomer-plugin-simple'
       """

data/lib/genomer/files.rb

@@ -0,0 +1,51 @@
+require 'genomer/version'
+
+class Genomer::Files
+  class << self
+
+    def gemfile
+      version = Genomer::VERSION.split('.')[0..1].<<(0).join('.')
+      <<-EOF.unindent
+        source :rubygems
+
+        gem 'genomer',    '~> #{version}'
+      EOF
+    end
+
+    def scaffold_yml
+      <<-EOF.unindent
+        # Specify your genome scaffold in YAML format here. Reference nucleotide
+        # sequences in the 'sequences.fna' file using the first space delimited
+        # word of each fasta header.
+        #
+        # Go to http://next.gs/getting-started/ to start writing genome scaffold
+        # files.
+        #
+        # A simple one contig example is also provided below. Delete this as you
+        # start writing your own scaffold.
+        ---
+          -
+            sequence:
+              source: "contig1"
+      EOF
+    end
+
+    def sequence_fna
+      <<-EOF.unindent
+        ; Add your assembled contigs and scaffolds sequences to this file.
+        ; These sequences can be referenced in the 'scaffold.yml' file
+        ; using the first space delimited word in each fasta header.
+        > contig1
+        ATGC
+      EOF
+    end
+
+    def annotations_gff
+      <<-EOF.unindent
+      ##gff-version   3
+      ## Add your gff3 formatted annotations to this file
+      EOF
+    end
+
+  end
+end

data/lib/genomer/runtime.rb

@@ -87,9 +87,22 @@ class Genomer::Runtime
     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
+
+    require 'genomer/files'
+
+    Dir.mkdir project_name
+    Dir.mkdir File.join(project_name,'assembly')
+
+
+    File.open(File.join(project_name,'Gemfile'),'w') do |file|
+      file.print Genomer::Files.gemfile
+    end
+
+    ['scaffold.yml','sequence.fna','annotations.gff'].each do |name|
+      File.open(File.join(project_name,'assembly',name),'w') do |file|
+        file.print Genomer::Files.send(name.gsub('.','_').to_sym)
+      end
     end
   end
 

data/lib/genomer/version.rb

@@ -1,3 +1,3 @@
 module Genomer
-  VERSION = "0.0.6"
+  VERSION = "0.0.7"
 end

data/spec/genomer/runtime_spec.rb

@@ -60,6 +60,60 @@ describe Genomer::Runtime do
           File.exists?(File.join('project_name','assembly')).should be_true
         end
 
+        it "should create a 'scaffold.yml' file" do
+          file = File.join('project_name','assembly','scaffold.yml')
+          File.exists?(file).should be_true
+          File.read(file).should == <<-EOF.unindent
+            # Specify your genome scaffold in YAML format here. Reference nucleotide
+            # sequences in the 'sequences.fna' file using the first space delimited
+            # word of each fasta header.
+            #
+            # Go to http://next.gs/getting-started/ to start writing genome scaffold
+            # files.
+            #
+            # A simple one contig example is also provided below. Delete this as you
+            # start writing your own scaffold.
+            ---
+              -
+                sequence:
+                  source: "contig1"
+          EOF
+        end
+
+        it "should create a 'sequence.fna' file" do
+          file = File.join('project_name','assembly','sequence.fna')
+          File.exists?(file).should be_true
+          File.read(file).should == <<-EOF.unindent
+            ; Add your assembled contigs and scaffolds sequences to this file.
+            ; These sequences can be referenced in the 'scaffold.yml' file
+            ; using the first space delimited word in each fasta header.
+            > contig1
+            ATGC
+          EOF
+        end
+
+        it "should create a 'annotations.gff' file" do
+          file = File.join('project_name','assembly','annotations.gff')
+
+          File.exists?(file).should be_true
+          File.read(file).should == <<-EOF.unindent
+            ##gff-version   3
+            ## Add your gff3 formatted annotations to this file
+          EOF
+        end
+
+        it "should create a 'Gemfile' file" do
+          file    = File.join('project_name','Gemfile')
+          version = Genomer::VERSION.split('.')[0..1] << '0'
+
+
+          File.exists?(file).should be_true
+          File.read(file).should == <<-EOF.unindent
+            source :rubygems
+
+            gem 'genomer',    '~> #{version.join('.')}'
+          EOF
+        end
       end
 
       describe "when project already exists" do

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: genomer
 version: !ruby/object:Gem::Version
-  version: 0.0.6
+  version: 0.0.7
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-05-31 00:00:00.000000000 Z
+date: 2012-06-06 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -238,10 +238,9 @@ files:
 - cucumber.yml
 - features/api/annotation_ids.feature
 - features/api/annotation_location.feature
-- features/api/scaffold.feature
-- features/cli/create.feature
 - features/cli/error.feature
 - features/cli/help.feature
+- features/cli/init.feature
 - features/cli/man.feature
 - features/cli/plugins.feature
 - features/step_definitions/genomer_steps.rb
@@ -253,6 +252,7 @@ files:
 - genomer.gemspec
 - lib/genomer.rb
 - lib/genomer/error.rb
+- lib/genomer/files.rb
 - lib/genomer/plugin.rb
 - lib/genomer/runtime.rb
 - lib/genomer/version.rb
@@ -275,7 +275,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -2849054132154778027
+      hash: -2433583334421431310
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:

data/features/api/scaffold.feature

@@ -1,38 +0,0 @@
-Feature: Plugins accessing the scaffold in a genomer project
-  In order to access the scaffold in a genomer plugin
-  A plugin developer can access the scaffold using the #scaffold method
-  So that the scaffold can be used
-
-  @disable-bundler
-  Scenario: Plugin accessing the scaffold
-    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
-      ATGC
-      >contig2
-      ATGC
-      """
-     When I run the genomer command with the arguments "simple describe"
-     Then the exit status should be 0
-      And the output should contain:
-     """
-     The scaffold contains 2 entries
-     """

data/features/cli/create.feature

@@ -1,19 +0,0 @@
-Feature: Creating a new genomer project
-  In order to build a genome
-  A user can create a new genomer project
-  So that they can use the genomer commands and organise their data
-
-  Scenario: Creating a new project
-    When I run the genomer command with the arguments "init project"
-    Then the exit status should be 0
-    And a directory named "project" should exist
-    And a directory named "project/assembly" should exist
-
-  Scenario: Creating a new project where the directory already exists
-    Given a directory named "project"
-    When I run the genomer command with the arguments "init project"
-    Then the exit status should be 1
-    And the stderr should contain:
-    """
-    Error. Directory 'project' already exists.
-    """