genomer-plugin-summary 0.0.3 → 0.0.4

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

@@ -0,0 +1,211 @@
+require 'spec_helper'
+require 'genomer-plugin-summary/contigs'
+
+describe GenomerPluginSummary::Contigs do
+
+  def row(num,start,stop,percent,gc)
+    {:id      => num,
+     :start   => start,
+     :stop    => stop,
+     :size    => (stop - start) + 1,
+     :percent => percent,
+     :type    => :contig,
+     :gc      => gc}
+  end
+
+  describe "#tabulate" do
+
+    subject do
+      described_class.new([],{}).tabulate(contigs,total,flags)
+    end
+
+    let(:flags) do
+      {}
+    end
+
+    context "passed an empty array" do
+
+      let(:contigs) do
+        []
+      end
+
+      let(:total) do
+        {:start   => 0,
+         :stop    => 0,
+         :size    => 0,
+         :percent => 0,
+         :gc      => 0 }
+      end
+
+      it do
+        should ==<<-EOS.unindent!
+      +--------+------------+------------+------------+----------+--------+
+      |                         Scaffold Contigs                          |
+      +--------+------------+------------+------------+----------+--------+
+      | Contig | Start (bp) |  End (bp)  | Size (bp)  | Size (%) | GC (%) |
+      +--------+------------+------------+------------+----------+--------+
+      +--------+------------+------------+------------+----------+--------+
+      |    All |          0 |          0 |          0 |     0.00 |   0.00 |
+      +--------+------------+------------+------------+----------+--------+
+        EOS
+      end
+
+    end
+
+    context "passed an array with a single row" do
+
+      let(:contigs) do
+        [row(1,1,4,100.0,50.0)]
+      end
+
+      let(:total) do
+        {:start   => '1',
+         :stop    => '4',
+         :size    => '4',
+         :percent => 100.0,
+         :gc      => 50.0 }
+      end
+
+      it do
+        should ==<<-EOS.unindent!
+      +--------+------------+------------+------------+----------+--------+
+      |                         Scaffold Contigs                          |
+      +--------+------------+------------+------------+----------+--------+
+      | Contig | Start (bp) |  End (bp)  | Size (bp)  | Size (%) | GC (%) |
+      +--------+------------+------------+------------+----------+--------+
+      |      1 |          1 |          4 |          4 |   100.00 |  50.00 |
+      +--------+------------+------------+------------+----------+--------+
+      |    All |          1 |          4 |          4 |   100.00 |  50.00 |
+      +--------+------------+------------+------------+----------+--------+
+        EOS
+      end
+
+    end
+
+    context "passed a array with two rows" do
+
+      let(:contigs) do
+        [row(1,1,4,100.0,50.0),
+         row(2,1,4,100.0,50.0)]
+      end
+
+      let(:total) do
+        {:start   => '1',
+         :stop    => '4',
+         :size    => '4',
+         :percent => 100.0,
+         :gc      => 50.0 }
+      end
+
+      it do
+        should ==<<-EOS.unindent!
+      +--------+------------+------------+------------+----------+--------+
+      |                         Scaffold Contigs                          |
+      +--------+------------+------------+------------+----------+--------+
+      | Contig | Start (bp) |  End (bp)  | Size (bp)  | Size (%) | GC (%) |
+      +--------+------------+------------+------------+----------+--------+
+      |      1 |          1 |          4 |          4 |   100.00 |  50.00 |
+      |      2 |          1 |          4 |          4 |   100.00 |  50.00 |
+      +--------+------------+------------+------------+----------+--------+
+      |    All |          1 |          4 |          4 |   100.00 |  50.00 |
+      +--------+------------+------------+------------+----------+--------+
+        EOS
+      end
+
+    end
+
+    context "passed the csv output option" do
+
+      let(:flags) do
+        {:output => 'csv'}
+      end
+
+      let(:contigs) do
+        [row(1,1,4,100.0,50.0),
+         row(2,1,4,100.0,50.0)]
+      end
+
+      let(:total) do
+        {:start   => '1',
+         :stop    => '4',
+         :size    => '4',
+         :percent => 100.0,
+         :gc      => 50.0 }
+      end
+
+      it do
+        should ==<<-EOS.unindent!
+          contig,start_bp,end_bp,size_bp,size_%,gc_%
+          1,1,4,4,100.00,50.00
+          2,1,4,4,100.00,50.00
+          all,1,4,4,100.00,50.00
+        EOS
+      end
+
+    end
+
+  end
+
+  describe "#calculate" do
+
+    subject do
+      described_class.new([],{}).calculate(scaffold)
+    end
+
+    context "passed an empty array" do
+      let(:scaffold) do
+        []
+      end
+
+      it do
+        should == []
+      end
+    end
+
+    context "passed one sequence" do
+      let(:scaffold) do
+        [sequence('AAAGGG','contig1')]
+      end
+
+      it do
+        should == [row(1,1,6,100.0,50.0)]
+      end
+    end
+
+    context "passed two sequences" do
+      let(:scaffold) do
+        [sequence('AAAGGG','contig1'),
+         sequence('AAAGGG','contig2')]
+      end
+
+      it do
+        should == [row(1, 1, 12, 100.0, 50.0)]
+      end
+    end
+
+    context "passed two sequences separated by a gap" do
+      let(:scaffold) do
+        [sequence('AAAGGG','contig1'),
+         unresolved('NNNNNNNN'),
+         sequence('AAAGGG','contig2')]
+      end
+
+      it do
+        should == [row(1, 1,  6,  30.0, 50.0),
+                   row(2, 15, 20, 30.0, 50.0)]
+      end
+    end
+
+    context "passed one contig containing a gap" do
+      let(:scaffold) do
+        [sequence('AAAGGGNNNNNNNNAAAGGG','contig1')]
+      end
+
+      it do
+        should == [row(1, 1,  6,  30.0, 50.0),
+                   row(2, 15, 20, 30.0, 50.0)]
+      end
+    end
+
+  end
+end

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

@@ -0,0 +1,383 @@
+require 'spec_helper'
+require 'genomer-plugin-summary/enumerators'
+
+describe GenomerPluginSummary::Enumerators do
+
+  describe "#enumerator_for" do
+
+    subject do
+      o = Object.new
+      o.extend described_class
+      o.enumerator_for(type,scaffold).to_a
+    end
+
+    describe "sequence" do
+
+      let(:type){ :sequence }
+
+      context "with an empty scaffold" do
+
+        let(:scaffold) do
+          []
+        end
+
+        it do
+          should == []
+        end
+
+      end
+
+      context "with a single unresolved region" do
+
+        let(:scaffold) do
+          [unresolved('NNNN')]
+        end
+
+        it do
+          should == []
+        end
+
+      end
+
+      context "with a single sequence region" do
+
+        let(:scaffold) do
+          [sequence('ATGC','ctg1')]
+        end
+
+        it do
+          should == [
+            {:start     => 1,
+              :stop     => 4,
+              :id       => 'ctg1',
+              :sequence => 'ATGC',
+              :type     => :sequence}
+          ]
+        end
+
+      end
+
+      context "with two sequence regions" do
+
+        let(:scaffold) do
+          [sequence('ATGC','ctg1'),sequence('ATGC','ctg2')]
+        end
+
+        it do
+          should == [
+            { :start    => 1,
+              :stop     => 4,
+              :id       => 'ctg1',
+              :sequence => 'ATGC',
+              :type     => :sequence},
+            { :start    => 5,
+              :stop     => 8,
+              :id       => 'ctg2',
+              :sequence => 'ATGC',
+              :type     => :sequence}
+          ]
+        end
+
+      end
+
+      context "with two sequence regions separated by a gap" do
+
+        let(:scaffold) do
+          [sequence('ATGC','ctg1'), unresolved('NNNN'), sequence('ATGC','ctg2')]
+        end
+
+        it do
+          should == [
+            { :start    => 1,
+              :stop     => 4,
+              :id       => 'ctg1',
+              :sequence => 'ATGC',
+              :type     => :sequence},
+            { :start    => 9,
+              :stop     => 12,
+              :id       => 'ctg2',
+              :sequence => 'ATGC',
+              :type     => :sequence}
+          ]
+        end
+
+      end
+
+    end
+
+    describe "contig" do
+
+      let(:type){ :contig }
+
+      context "with an empty scaffold" do
+
+        let(:scaffold) do
+          []
+        end
+
+        it do
+          should == []
+        end
+
+      end
+
+      context "with a single unresolved region" do
+
+        let(:scaffold) do
+          [unresolved('NNNN')]
+        end
+
+        it do
+          should == []
+        end
+
+      end
+
+      context "with a single sequence region" do
+
+        let(:scaffold) do
+          [sequence('ATGC','ctg1')]
+        end
+
+        it do
+          should == [
+            {:start    => 1,
+             :stop     => 4,
+             :id       => 1,
+             :sequence => 'ATGC',
+             :type     => :contig}
+          ]
+        end
+
+      end
+
+      context "with two sequence regions" do
+
+        let(:scaffold) do
+          [sequence('ATGC','ctg1'),sequence('ATGC','ctg2')]
+        end
+
+        it do
+          should == [
+            {:start    => 1,
+             :stop     => 8,
+             :id       => 1,
+             :sequence => 'ATGCATGC',
+             :type     => :contig}
+          ]
+        end
+
+      end
+
+      context "with two sequence regions separated by a gap" do
+
+        let(:scaffold) do
+          [sequence('ATGC','ctg1'), unresolved('NNNN'), sequence('ATGC','ctg2')]
+        end
+
+        it do
+          should == [
+            { :start    => 1,
+              :stop     => 4,
+              :id       => 1,
+              :sequence => 'ATGC',
+              :type     => :contig},
+            { :start    => 9,
+              :stop     => 12,
+              :id       => 2,
+              :sequence => 'ATGC',
+              :type     => :contig}
+          ]
+        end
+
+      end
+
+      context "with two sequence regions, one containing a gap" do
+
+        let(:scaffold) do
+          [sequence('ATGCNNNNATGC','ctg1'), sequence('ATGC','ctg2')]
+        end
+
+        it do
+          should == [
+            { :start    => 1,
+              :stop     => 4,
+              :id       => 1,
+              :sequence => 'ATGC',
+              :type     => :contig},
+            { :start    => 9,
+              :stop     => 16,
+              :id       => 2,
+              :sequence => 'ATGCATGC',
+              :type     => :contig}
+          ]
+        end
+
+      end
+
+    end
+
+    describe "unresolved" do
+
+      let(:type){ :unresolved }
+
+      context "with an empty scaffold" do
+
+        let(:scaffold) do
+          []
+        end
+
+        it do
+          should == []
+        end
+
+      end
+
+      context "with a single unresolved region" do
+
+        let(:scaffold) do
+          [unresolved('NNNN')]
+        end
+
+        it do
+          should == [
+            { :start    => 1,
+              :stop     => 4,
+              :id       => nil,
+              :sequence => 'NNNN',
+              :type     => :unresolved},
+          ]
+        end
+
+      end
+
+      context "with a single sequence region" do
+
+        let(:scaffold) do
+          [sequence('ATGC','ctg1')]
+        end
+
+        it do
+          should == []
+        end
+
+      end
+
+      context "with two sequence regions separated by a gap" do
+
+        let(:scaffold) do
+          [sequence('ATGC','ctg1'), unresolved('NNNN'), sequence('ATGC','ctg2')]
+        end
+
+        it do
+          should == [
+            { :start    => 5,
+              :stop     => 8,
+              :id       => nil,
+              :sequence => 'NNNN',
+              :type     => :unresolved},
+          ]
+        end
+
+      end
+
+    end
+
+    describe "gap" do
+
+      let(:type){ :gap }
+
+      context "with an empty scaffold" do
+
+        let(:scaffold) do
+          []
+        end
+
+        it do
+          should == []
+        end
+
+      end
+
+      context "with a single unresolved region" do
+
+        let(:scaffold) do
+          [unresolved('NNNN')]
+        end
+
+        it do
+          should == [
+            { :start    => 1,
+              :stop     => 4,
+              :id       => 1,
+              :sequence => 'NNNN',
+              :type     => :gap},
+          ]
+        end
+
+      end
+
+      context "with a single sequence region" do
+
+        let(:scaffold) do
+          [sequence('ATGC','ctg1')]
+        end
+
+        it do
+          should == []
+        end
+
+      end
+
+      context "with two sequence regions" do
+
+        let(:scaffold) do
+          [sequence('ATGC','ctg1'),sequence('ATGC','ctg2')]
+        end
+
+        it do
+          should == []
+        end
+
+      end
+
+      context "with two sequence regions separated by a gap" do
+
+        let(:scaffold) do
+          [sequence('ATGC','ctg1'), unresolved('NNNN'), sequence('ATGC','ctg2')]
+        end
+
+        it do
+          should == [
+            { :start    => 5,
+              :stop     => 8,
+              :id       => 1,
+              :sequence => 'NNNN',
+              :type     => :gap},
+          ]
+        end
+
+      end
+
+      context "with two sequence regions, one containing a gap" do
+
+        let(:scaffold) do
+          [sequence('ATGCNNNNATGC','ctg1'), sequence('ATGC','ctg2')]
+        end
+
+        it do
+          should == [
+            { :start    => 5,
+              :stop     => 8,
+              :id       => 1,
+              :sequence => 'NNNN',
+              :type     => :gap},
+          ]
+        end
+
+      end
+
+    end
+  end
+
+end