genomer-plugin-summary 0.0.3 → 0.0.4

data/spec/spec_helper.rb

@@ -16,7 +16,7 @@ RSpec.configure do |config|
   def sequence(seq, source=nil)
     s = mock!
     stub(s).sequence{ seq }
-    stub(s).source{ source } if source
+    stub(s).source{ source }
     stub(s).entry_type{ :sequence }
     s
   end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: genomer-plugin-summary
 version: !ruby/object:Gem::Version
-  version: 0.0.3
+  version: 0.0.4
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-10-19 00:00:00.000000000 Z
+date: 2012-10-31 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: genomer
@@ -168,23 +168,30 @@ files:
 - README.md
 - Rakefile
 - VERSION
+- features/contigs.feature
 - features/gaps.feature
-- features/scaffold.feature
+- features/genome.feature
 - features/sequences.feature
 - features/support/env.rb
 - features/support/genomer_steps.rb
 - genomer-plugin-summary.gemspec
 - lib/genomer-plugin-summary.rb
+- lib/genomer-plugin-summary/contigs.rb
+- lib/genomer-plugin-summary/enumerators.rb
+- lib/genomer-plugin-summary/format.rb
 - lib/genomer-plugin-summary/gaps.rb
+- lib/genomer-plugin-summary/genome.rb
 - lib/genomer-plugin-summary/metrics.rb
-- lib/genomer-plugin-summary/scaffold.rb
 - lib/genomer-plugin-summary/sequences.rb
 - man/genomer-summary-gaps.ronn
 - man/genomer-summary.ronn
 - spec/genomer-plugin-summary_spec.rb
+- spec/genomer-plugin-summary_spec/contigs_spec.rb
+- spec/genomer-plugin-summary_spec/enumerators_spec.rb
+- spec/genomer-plugin-summary_spec/format_spec.rb
 - spec/genomer-plugin-summary_spec/gaps_spec.rb
+- spec/genomer-plugin-summary_spec/genome_spec.rb
 - spec/genomer-plugin-summary_spec/metrics_spec.rb
-- spec/genomer-plugin-summary_spec/scaffold_spec.rb
 - spec/genomer-plugin-summary_spec/sequences_spec.rb
 - spec/spec_helper.rb
 homepage: ''
@@ -201,7 +208,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 4220695143332306969
+      hash: 2735699573861550577
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:
@@ -210,7 +217,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 4220695143332306969
+      hash: 2735699573861550577
 requirements: []
 rubyforge_project: 
 rubygems_version: 1.8.23
@@ -218,14 +225,18 @@ signing_key:
 specification_version: 3
 summary: Generates reports on the status of the genomer project
 test_files:
+- features/contigs.feature
 - features/gaps.feature
-- features/scaffold.feature
+- features/genome.feature
 - features/sequences.feature
 - features/support/env.rb
 - features/support/genomer_steps.rb
 - spec/genomer-plugin-summary_spec.rb
+- spec/genomer-plugin-summary_spec/contigs_spec.rb
+- spec/genomer-plugin-summary_spec/enumerators_spec.rb
+- spec/genomer-plugin-summary_spec/format_spec.rb
 - spec/genomer-plugin-summary_spec/gaps_spec.rb
+- spec/genomer-plugin-summary_spec/genome_spec.rb
 - spec/genomer-plugin-summary_spec/metrics_spec.rb
-- spec/genomer-plugin-summary_spec/scaffold_spec.rb
 - spec/genomer-plugin-summary_spec/sequences_spec.rb
 - spec/spec_helper.rb

data/features/scaffold.feature

@@ -1,122 +0,0 @@
-Feature: Producing a summary of the scaffold
-  In order to have an overview of the scaffold
-  A user can use the "scaffod" command
-  to generate the a tabular output of the scaffold
-
-  Scenario: A scaffold with a single sequence
-    Given I create a new genomer project
-      And I write to "assembly/scaffold.yml" with:
-      """
-      ---
-        -
-          sequence:
-            source: contig0001
-      """
-      And I write to "assembly/sequence.fna" with:
-      """
-      >contig0001
-      ATGC
-      """
-     When I run `genomer summary scaffold`
-     Then the exit status should be 0
-      And the output should contain:
-      """
-      +--------------+-----------+
-      |         Scaffold         |
-      +--------------+-----------+
-      | Contigs (#)  |         1 |
-      | Gaps (#)     |         0 |
-      +--------------+-----------+
-      | Size (bp)    |         4 |
-      | Contigs (bp) |         4 |
-      | Gaps (bp)    |         0 |
-      +--------------+-----------+
-      | G+C (%)      |     50.00 |
-      | Contigs (%)  |    100.00 |
-      | Gaps (%)     |      0.00 |
-      +--------------+-----------+
-
-      """
-
-  Scenario: A scaffold with a two sequences
-    Given I create a new genomer project
-      And I write to "assembly/scaffold.yml" with:
-      """
-      ---
-        -
-          sequence:
-            source: contig0001
-        -
-          sequence:
-            source: contig0002
-      """
-      And I write to "assembly/sequence.fna" with:
-      """
-      >contig0001
-      ATGC
-      >contig0002
-      GGGC
-      """
-     When I run `genomer summary scaffold`
-     Then the exit status should be 0
-      And the output should contain:
-      """
-      +--------------+-----------+
-      |         Scaffold         |
-      +--------------+-----------+
-      | Contigs (#)  |         2 |
-      | Gaps (#)     |         0 |
-      +--------------+-----------+
-      | Size (bp)    |         8 |
-      | Contigs (bp) |         8 |
-      | Gaps (bp)    |         0 |
-      +--------------+-----------+
-      | G+C (%)      |     75.00 |
-      | Contigs (%)  |    100.00 |
-      | Gaps (%)     |      0.00 |
-      +--------------+-----------+
-
-      """
-
-  Scenario: A scaffold with a two sequences and a gap
-    Given I create a new genomer project
-      And I write to "assembly/scaffold.yml" with:
-      """
-      ---
-        -
-          sequence:
-            source: contig0001
-        -
-          unresolved:
-            length: 5
-        -
-          sequence:
-            source: contig0002
-      """
-      And I write to "assembly/sequence.fna" with:
-      """
-      >contig0001
-      ATGC
-      >contig0002
-      GGGC
-      """
-     When I run `genomer summary scaffold`
-     Then the exit status should be 0
-      And the output should contain:
-      """
-      +--------------+-----------+
-      |         Scaffold         |
-      +--------------+-----------+
-      | Contigs (#)  |         2 |
-      | Gaps (#)     |         1 |
-      +--------------+-----------+
-      | Size (bp)    |        13 |
-      | Contigs (bp) |         8 |
-      | Gaps (bp)    |         5 |
-      +--------------+-----------+
-      | G+C (%)      |     75.00 |
-      | Contigs (%)  |     61.54 |
-      | Gaps (%)     |     38.46 |
-      +--------------+-----------+
-
-      """

data/lib/genomer-plugin-summary/scaffold.rb

@@ -1,56 +0,0 @@
-require 'genomer'
-require 'genomer-plugin-summary/metrics'
-require 'terminal-table'
-
-class GenomerPluginSummary::Scaffold < Genomer::Plugin
-  include GenomerPluginSummary::Metrics
-
-  LAYOUT = [
-    {:name => 'Contigs (#)',  :entry_type => :sequence,   :method => :count},
-    {:name => 'Gaps (#)',     :entry_type => :unresolved, :method => :count},
-    :separator,
-    {:name => 'Size (bp)',    :entry_type => :all,        :method => :length},
-    {:name => 'Contigs (bp)', :entry_type => :sequence,   :method => :length},
-    {:name => 'Gaps (bp)',    :entry_type => :unresolved, :method => :length},
-    :separator,
-    {:name => 'G+C (%)',      :entry_type => :all,        :method => :gc_content},
-    {:name => 'Contigs (%)',  :entry_type => :sequence,   :method => :percent},
-    {:name => 'Gaps (%)',     :entry_type => :unresolved, :method => :percent}
-  ]
-
-  def run
-    tabulate calculate_metrics(LAYOUT, scaffold)
-  end
-
-  def title
-    'Scaffold'
-  end
-
-  def tabulate(data)
-    table = Terminal::Table.new(:title => title) do |t|
-      data.each do |(k,v)|
-        t << if k == :separator
-               :separator
-             else
-               v = sprintf('%#.2f',v) if v.class == Float
-               [k.ljust(12),v.to_s.rjust(9)]
-             end
-      end
-    end
-
-    table.align_column 0, :left
-    table.align_column 1, :right
-    table.to_s
-  end
-
-  def calculate_metrics(specs,scaffold)
-    specs.map do |spec|
-      if spec == :separator
-        spec
-      else
-        [spec[:name], send(spec[:method],spec[:entry_type],scaffold)]
-      end
-    end
-  end
-
-end