genomer-plugin-summary 0.0.3 → 0.0.4

data/spec/genomer-plugin-summary_spec/format_spec.rb

@@ -0,0 +1,285 @@
+require 'spec_helper'
+require 'genomer-plugin-summary/format'
+
+describe GenomerPluginSummary::Format do
+
+  subject do
+    o = Object.new
+    o.extend described_class
+    o.table(data,options.merge(:output => output))
+  end
+
+  describe "#table" do
+
+    let(:data) do
+      [['Contigs (#)',1.0],
+        :separator,
+        ['Gaps (#)',0]]
+    end
+
+    context "passed no output option" do
+
+      let(:output) do
+        nil
+      end
+
+      context "without any addtional options" do
+
+        let(:options) do
+          {}
+        end
+
+        it do
+          should ==<<-EOS.unindent!
+        +-------------+-----+
+        | Contigs (#) | 1.0 |
+        +-------------+-----+
+        | Gaps (#)    | 0   |
+        +-------------+-----+
+          EOS
+        end
+      end
+
+      context "the header option" do
+
+        let(:options) do
+          {:title => 'Scaffold' }
+        end
+
+        it do
+          should ==<<-EOS.unindent!
+      +-------------+-----+
+      |     Scaffold      |
+      +-------------+-----+
+      | Contigs (#) | 1.0 |
+      +-------------+-----+
+      | Gaps (#)    | 0   |
+      +-------------+-----+
+          EOS
+        end
+
+      end
+
+      context "with the justification option" do
+
+        let(:options) do
+          {:justification => {
+            0 => :left,
+            1 => :right
+          }}
+        end
+
+        it do
+          should ==<<-EOS.unindent!
+      +-------------+-----+
+      | Contigs (#) | 1.0 |
+      +-------------+-----+
+      | Gaps (#)    |   0 |
+      +-------------+-----+
+          EOS
+        end
+      end
+
+      context "with the width option" do
+
+        let(:options) do
+          {:width         => { 0 => 15, 1 => 10 },
+            :justification => { 1 => :right }}
+        end
+
+        it do
+          should ==<<-EOS.unindent!
+      +-----------------+------------+
+      | Contigs (#)     |        1.0 |
+      +-----------------+------------+
+      | Gaps (#)        |          0 |
+      +-----------------+------------+
+          EOS
+        end
+
+      end
+
+      context "with the format option" do
+
+        let(:options) do
+          {:format => { 1 => '%#.2f'}}
+        end
+
+        it do
+          should ==<<-EOS.unindent!
+      +-------------+------+
+      | Contigs (#) | 1.00 |
+      +-------------+------+
+      | Gaps (#)    | 0.00 |
+      +-------------+------+
+          EOS
+        end
+
+      end
+
+      context "with the format option as a lambda" do
+
+        let(:options) do
+          {:format => { 1 => lambda{|i| i.class == Float ? sprintf('%#.2f',i) : i }}}
+        end
+
+        it do
+          should ==<<-EOS.unindent!
+      +-------------+------+
+      | Contigs (#) | 1.00 |
+      +-------------+------+
+      | Gaps (#)    | 0    |
+      +-------------+------+
+          EOS
+        end
+
+      end
+
+      context "with the header option" do
+
+        let(:options) do
+          {:headers => ['One','Two']}
+        end
+
+        it do
+          should ==<<-EOS.unindent!
+      +-------------+-----+
+      |     One     | Two |
+      +-------------+-----+
+      | Contigs (#) | 1.0 |
+      +-------------+-----+
+      | Gaps (#)    | 0   |
+      +-------------+-----+
+          EOS
+        end
+
+      end
+
+    context "with the header and width options but no data" do
+
+      let(:options) do
+        {:headers => ['One','Two'],
+         :width   => { 0 => 15, 1 => 10 }}
+      end
+
+      let(:data) do
+        []
+      end
+
+      it do
+        should ==<<-EOS.unindent!
+      +-----------------+------------+
+      |       One       |    Two     |
+      +-----------------+------------+
+      +-----------------+------------+
+        EOS
+      end
+
+    end
+
+  end
+
+    context "passed the csv output option" do
+
+      let(:output) do
+        'csv'
+      end
+
+      context "without any additional options" do
+
+        let(:options) do
+          {}
+        end
+
+        it do
+          should ==<<-EOS.unindent!
+            contigs_#,1.0
+            gaps_#,0
+          EOS
+        end
+      end
+
+      context "with the justification option" do
+
+        let(:options) do
+          {:justification => {
+            0 => :left,
+            1 => :right
+          }}
+        end
+
+        it do
+          should ==<<-EOS.unindent!
+            contigs_#,1.0
+            gaps_#,0
+          EOS
+        end
+      end
+
+      context "with the width option" do
+
+        let(:options) do
+          {:width         => { 0 => 15, 1 => 10 },
+           :justification => { 1 => :right }}
+        end
+
+        it do
+          should ==<<-EOS.unindent!
+            contigs_#,1.0
+            gaps_#,0
+          EOS
+        end
+
+      end
+
+      context "with the header option" do
+
+        let(:options) do
+          {:headers => ['One','Two']}
+        end
+
+        it do
+          should ==<<-EOS.unindent!
+            one,two
+            contigs_#,1.0
+            gaps_#,0
+          EOS
+        end
+
+      end
+
+      context "with the format option" do
+
+        let(:options) do
+          {:format => { 1 => '%#.2f'}}
+        end
+
+        it do
+          should ==<<-EOS.unindent!
+            contigs_#,1.00
+            gaps_#,0.00
+          EOS
+        end
+
+      end
+
+      context "with the format option as a lambda" do
+
+        let(:options) do
+          {:format => { 1 => lambda{|i| i.class == Float ? sprintf('%#.2f',i) : i }}}
+        end
+
+        it do
+          should ==<<-EOS.unindent!
+            contigs_#,1.00
+            gaps_#,0
+          EOS
+        end
+
+      end
+
+    end
+
+  end
+
+end

data/spec/genomer-plugin-summary_spec/gaps_spec.rb

@@ -6,12 +6,16 @@ describe GenomerPluginSummary::Gaps do
   describe "#tabulate" do
 
     subject do
-      described_class.new([],{}).tabulate(contigs) + "\n"
+      described_class.new([],{}).tabulate(sequences,flags)
+    end
+
+    let(:flags) do
+      {}
     end
 
     context "passed an empty array" do
 
-      let(:contigs) do
+      let(:sequences) do
         []
       end
 
@@ -30,7 +34,7 @@ describe GenomerPluginSummary::Gaps do
 
     context "passed an array with one entry" do
 
-      let(:contigs) do
+      let(:sequences) do
         [{:number => 1, :length => 1, :start => 1, :end => 1, :type => :contig}]
       end
 
@@ -50,7 +54,7 @@ describe GenomerPluginSummary::Gaps do
 
     context "passed an array with two entries" do
 
-      let(:contigs) do
+      let(:sequences) do
         [{:number => 1, :length => 1, :start => 1, :end => 1, :type => :contig},
          {:number => 2, :length => 2, :start => 2, :end => 2, :type => :unresolved}]
       end
@@ -70,6 +74,27 @@ describe GenomerPluginSummary::Gaps do
 
     end
 
+    context "passed the csv option" do
+
+      let(:flags) do
+        {:output => 'csv'}
+      end
+
+      let(:sequences) do
+        [{:number => 1, :length => 1, :start => 1, :end => 1, :type => :contig},
+         {:number => 2, :length => 2, :start => 2, :end => 2, :type => :unresolved}]
+      end
+
+      it do
+        should ==<<-EOS.unindent!
+          number,length,start,end,type
+          1,1,1,1,contig
+          2,2,2,2,unresolved
+        EOS
+      end
+
+    end
+
   end
 
   describe "#determine_gaps" do
@@ -104,7 +129,7 @@ describe GenomerPluginSummary::Gaps do
       end
     end
 
-    context "a scaffold with a two contigs containing gaps" do
+    context "a scaffold with a two sequences containing gaps" do
       let(:scaffold) do
         [sequence('AANNTT'), sequence('AANNTT')]
       end
@@ -116,7 +141,7 @@ describe GenomerPluginSummary::Gaps do
       end
     end
 
-    context "a scaffold with two contigs separated by an unresolved region" do
+    context "a scaffold with two sequences separated by an unresolved region" do
       let(:scaffold) do
         [sequence('AAT'),
          unresolved('NNNNNNNNNN'),
@@ -129,7 +154,7 @@ describe GenomerPluginSummary::Gaps do
       end
     end
 
-    context "a scaffold with a mixture of gapped contigs and unresolved regions" do
+    context "a scaffold with a mixture of gapped sequences and unresolved regions" do
       let(:scaffold) do
         [sequence('AAANNNTTT'),
          unresolved('NNNNNNNNNN'),

data/spec/genomer-plugin-summary_spec/{scaffold_spec.rb → genome_spec.rb}

@@ -1,20 +1,24 @@
 require 'spec_helper'
-require 'genomer-plugin-summary/scaffold'
+require 'genomer-plugin-summary/genome'
 
-describe GenomerPluginSummary::Scaffold do
+describe GenomerPluginSummary::Genome do
 
   describe "#tabulate" do
 
     subject do
-      described_class.new([],{}).tabulate(data) + "\n"
+      described_class.new([],{}).tabulate(data,flags)
+    end
+
+    let(:data) do
+      [['Contigs (#)',1.0],
+        :separator,
+          ['Gaps (#)',0]]
     end
 
     context "passed table data" do
 
-      let(:data) do
-        [['Contigs (#)',1.0],
-          :separator,
-         ['Gaps (#)',0]]
+      let(:flags) do
+        {}
       end
 
       it do
@@ -28,6 +32,21 @@ describe GenomerPluginSummary::Scaffold do
       +--------------+-----------+
         EOS
       end
+
+    end
+
+    context "passed table with the format option" do
+
+      let(:flags) do
+        {:output => 'csv'}
+      end
+
+      it do
+        should ==<<-EOS.unindent!
+          contigs_#,1.00
+          gaps_#,0
+        EOS
+      end
     end
   end
 

data/spec/genomer-plugin-summary_spec/metrics_spec.rb

@@ -70,6 +70,7 @@ describe GenomerPluginSummary::Metrics do
     end
 
   end
+
   describe "#count" do
 
     subject do
@@ -252,4 +253,67 @@ describe GenomerPluginSummary::Metrics do
 
   end
 
+  describe "#sequence_total" do
+
+    def row(name,start,stop,percent,gc)
+      {:id       => name,
+        :type     => :sequence,
+        :start    => start,
+        :stop     => stop,
+        :size     => (stop - start) + 1,
+        :percent  => percent,
+        :gc       => gc}
+    end
+
+    subject do
+      metric.sequence_total(sequences)
+    end
+
+    context "passed an empty array" do
+      let(:sequences) do
+        []
+      end
+
+      it do
+        should == {
+          :start   => 0,
+          :stop    => 0,
+          :size    => 0,
+          :percent => 0,
+          :gc      => 0 }
+      end
+    end
+
+    context "passed one entry" do
+      let(:sequences) do
+        [row('contig1',1,6,100.0,50.0)]
+      end
+
+      it do
+        should == {
+          :start   => 1,
+          :stop    => 6,
+          :size    => 6,
+          :percent => 100.0,
+          :gc      => 50.0 }
+      end
+    end
+
+    context "passed two entries less than 100% of the scaffold" do
+      let(:sequences) do
+        [row('contig1', 1,  6,  30.0, 50.0),
+         row('contig2', 15, 20, 30.0, 50.0)]
+      end
+
+      it do
+        should == {
+          :start   => 1,
+          :stop    => 20,
+          :size    => 12,
+          :percent => 60.0,
+          :gc      => 50.0 }
+      end
+    end
+  end
+
 end

data/spec/genomer-plugin-summary_spec/sequences_spec.rb

@@ -4,9 +4,10 @@ require 'genomer-plugin-summary/sequences'
 describe GenomerPluginSummary::Sequences do
 
   def row(name,start,stop,percent,gc)
-    {:sequence => name,
+    {:id       => name,
+     :type     => :sequence,
      :start    => start,
-     :end      => stop,
+     :stop     => stop,
      :size     => (stop - start) + 1,
      :percent  => percent,
      :gc       => gc}
@@ -15,7 +16,11 @@ describe GenomerPluginSummary::Sequences do
   describe "#tabulate" do
 
     subject do
-      described_class.new([],{}).tabulate(sequences,total) + "\n"
+      described_class.new([],{}).tabulate(sequences,total,flags)
+    end
+
+    let(:flags) do
+      {}
     end
 
     context "passed an empty array" do
@@ -25,11 +30,11 @@ describe GenomerPluginSummary::Sequences do
       end
 
       let(:total) do
-        {:start   => 'NA',
-         :end     => 'NA',
-         :size    => 'NA',
-         :percent => 'NA',
-         :gc      => 'NA' }
+        {:start   => 0,
+         :stop    => 0,
+         :size    => 0,
+         :percent => 0,
+         :gc      => 0 }
       end
 
       it do
@@ -37,10 +42,10 @@ describe GenomerPluginSummary::Sequences do
       +------------------+------------+------------+------------+----------+--------+
       |                             Scaffold Sequences                              |
       +------------------+------------+------------+------------+----------+--------+
-      | Sequence         | Start (bp) |  End (bp)  | Size (bp)  | Size (%) | GC (%) |
+      |     Sequence     | Start (bp) |  End (bp)  | Size (bp)  | Size (%) | GC (%) |
       +------------------+------------+------------+------------+----------+--------+
       +------------------+------------+------------+------------+----------+--------+
-      | All              |         NA |         NA |         NA |       NA |     NA |
+      | All              |          0 |          0 |          0 |     0.00 |   0.00 |
       +------------------+------------+------------+------------+----------+--------+
         EOS
       end
@@ -50,17 +55,12 @@ describe GenomerPluginSummary::Sequences do
     context "passed an array with a single row" do
 
       let(:sequences) do
-        [{:sequence   => 'contig1',
-          :start      => '1',
-          :end        => '4',
-          :size       => '4',
-          :percent    => 100.0,
-          :gc         => 50.0 }]
+        [row('contig1',1,4,100.0,50.0)]
       end
 
       let(:total) do
         {:start   => '1',
-         :end     => '4',
+         :stop    => '4',
          :size    => '4',
          :percent => 100.0,
          :gc      => 50.0 }
@@ -71,7 +71,7 @@ describe GenomerPluginSummary::Sequences do
       +------------------+------------+------------+------------+----------+--------+
       |                             Scaffold Sequences                              |
       +------------------+------------+------------+------------+----------+--------+
-      | Sequence         | Start (bp) |  End (bp)  | Size (bp)  | Size (%) | GC (%) |
+      |     Sequence     | Start (bp) |  End (bp)  | Size (bp)  | Size (%) | GC (%) |
       +------------------+------------+------------+------------+----------+--------+
       | contig1          |          1 |          4 |          4 |   100.00 |  50.00 |
       +------------------+------------+------------+------------+----------+--------+
@@ -85,23 +85,13 @@ describe GenomerPluginSummary::Sequences do
     context "passed a array with two rows" do
 
       let(:sequences) do
-        [{:sequence   => 'contig1',
-          :start      => '1',
-          :end        => '4',
-          :size       => '4',
-          :percent    => 100.0,
-          :gc         => 50.0 },
-         {:sequence   => 'contig2',
-          :start      => '1',
-          :end        => '4',
-          :size       => '4',
-          :percent    => 100.0,
-          :gc         => 50.0 }]
+        [row('contig1',1,4,100.0,50.0),
+         row('contig2',1,4,100.0,50.0)]
       end
 
       let(:total) do
         {:start   => '1',
-         :end     => '4',
+         :stop    => '4',
          :size    => '4',
          :percent => 100.0,
          :gc      => 50.0 }
@@ -112,7 +102,7 @@ describe GenomerPluginSummary::Sequences do
       +------------------+------------+------------+------------+----------+--------+
       |                             Scaffold Sequences                              |
       +------------------+------------+------------+------------+----------+--------+
-      | Sequence         | Start (bp) |  End (bp)  | Size (bp)  | Size (%) | GC (%) |
+      |     Sequence     | Start (bp) |  End (bp)  | Size (bp)  | Size (%) | GC (%) |
       +------------------+------------+------------+------------+----------+--------+
       | contig1          |          1 |          4 |          4 |   100.00 |  50.00 |
       | contig2          |          1 |          4 |          4 |   100.00 |  50.00 |
@@ -124,6 +114,36 @@ describe GenomerPluginSummary::Sequences do
 
     end
 
+    context "passed the csv output option" do
+
+      let(:flags) do
+        {:output => 'csv'}
+      end
+
+      let(:sequences) do
+        [row('contig1',1,4,100.0,50.0),
+         row('contig2',1,4,100.0,50.0)]
+      end
+
+      let(:total) do
+        {:start   => '1',
+         :stop    => '4',
+         :size    => '4',
+         :percent => 100.0,
+         :gc      => 50.0 }
+      end
+
+      it do
+        should ==<<-EOS.unindent!
+          sequence,start_bp,end_bp,size_bp,size_%,gc_%
+          contig1,1,4,4,100.00,50.00
+          contig2,1,4,4,100.00,50.00
+          all,1,4,4,100.00,50.00
+        EOS
+      end
+
+    end
+
   end
 
   describe "#calculate" do
@@ -179,57 +199,4 @@ describe GenomerPluginSummary::Sequences do
 
   end
 
-  describe "#total" do
-
-    subject do
-      described_class.new([],{}).total(sequences)
-    end
-
-    context "passed an empty array" do
-      let(:sequences) do
-        []
-      end
-
-      it do
-        should == {
-          :start   => 'NA',
-          :end     => 'NA',
-          :size    => 'NA',
-          :percent => 'NA',
-          :gc      => 'NA' }
-      end
-    end
-
-    context "passed one entry" do
-      let(:sequences) do
-        [row('contig1',1,6,100.0,50.0)]
-      end
-
-      it do
-        should == {
-          :start   => 1,
-          :end     => 6,
-          :size    => 6,
-          :percent => 100.0,
-          :gc      => 50.0 }
-      end
-    end
-
-    context "passed two entries less than 100% of the scaffold" do
-      let(:sequences) do
-        [row('contig1', 1,  6,  30.0, 50.0),
-         row('contig2', 15, 20, 30.0, 50.0)]
-      end
-
-      it do
-        should == {
-          :start   => 1,
-          :end     => 20,
-          :size    => 12,
-          :percent => 60.0,
-          :gc      => 50.0 }
-      end
-    end
-  end
-
 end