genomer-plugin-view 0.0.2

data/spec/genomer-view-plugin/agp_spec.rb

@@ -0,0 +1,79 @@
+require 'spec_helper'
+require 'genomer-plugin-view/agp'
+
+describe GenomerPluginView::Agp do
+
+  def contig(sequence)
+    s = mock!
+    stub(s).entry_type{ :sequence }
+    stub(s).sequence{ sequence }
+    s
+  end
+
+  def unresolved(length)
+    s = mock!
+    stub(s).entry_type{ :unresolved }
+    stub(s).sequence{ 'N' * length }
+    s
+  end
+
+  subject do
+    described_class.new(['agp'],{})
+  end
+
+  before do
+    mock(subject).scaffold do
+      contigs
+    end
+  end
+
+  context "where the scaffold contains a single contig" do
+
+    let (:contigs) do
+      [contig('AATGC')]
+    end
+
+    it "should return agp output" do
+      subject.run.should == <<-EOS.unindent
+        ##agp-version	2.0
+        scaffold	1	5	1	W	contig00001	1	5	+
+      EOS
+    end
+
+  end
+
+  context "where the scaffold contains a contig with a gap" do
+
+    let (:contigs) do
+      [contig('AAANNNGGG')]
+    end
+
+    it "should return agp output" do
+      subject.run.should == <<-EOS.unindent
+        ##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	+
+      EOS
+    end
+
+  end
+
+  context "where the scaffold contains an unresolved region" do
+
+    let (:contigs) do
+      [ contig('AAA'), unresolved(3), contig('TTT') ]
+    end
+
+    it "should return agp output" do
+      subject.run.should == <<-EOS.unindent
+        ##agp-version	2.0
+        scaffold	1	3	1	W	contig00001	1	3	+
+        scaffold	4	6	2	N	3	scaffold	yes	specified
+        scaffold	7	9	3	W	contig00002	1	3	+
+      EOS
+    end
+
+  end
+
+end

data/spec/genomer-view-plugin/fasta_spec.rb

@@ -0,0 +1,96 @@
+require 'spec_helper'
+require 'genomer-plugin-view/fasta'
+
+describe GenomerPluginView::Fasta do
+
+  before do
+    mock(subject).scaffold do
+      annotations
+    end
+  end
+
+  let (:annotations) do
+    [Sequence.new(:sequence => 'AAATGA')]
+  end
+
+  subject do
+    described_class.new(['fasta'],flags)
+  end
+
+  describe "with no options" do
+
+    let(:flags){ {} }
+
+    it "should return fasta output" do
+      subject.run.should == ">.\nAAATGA\n"
+    end
+
+  end
+
+  describe "run with the --identifier option" do
+
+    let(:flags){ {:identifier => 'name'} }
+
+    it "should return fasta output with the identifier" do
+      subject.run.should == ">name\nAAATGA\n"
+    end
+
+  end
+
+  describe "run with the --organism option" do
+
+    let(:flags){ {:organism => 'name'} }
+
+    it "should return fasta output with the organism modifier" do
+      subject.run.should == ">. [organism=name]\nAAATGA\n"
+    end
+
+  end
+
+  describe "run with the --strain option" do
+
+    let(:flags){ {:strain => 'name'} }
+
+    it "should return fasta output with the strain modifier" do
+      subject.run.should == ">. [strain=name]\nAAATGA\n"
+    end
+
+  end
+
+  describe "run with the identifier and a modifier option" do
+
+    let(:flags){ {:strain => 'isolate', :identifier => 'name'} }
+
+    it "should return fasta output with the strain modifier" do
+      subject.run.should == ">name [strain=isolate]\nAAATGA\n"
+    end
+
+  end
+
+  describe "run with the --contigs option" do
+
+    let(:flags){ {:contigs => true} }
+
+    context "with an ungapped contig scaffold" do
+
+      it "should return fasta output of the contig" do
+        subject.run.should == ">contig00001\nAAATGA\n"
+      end
+
+    end
+
+    context "with a gapped contig scaffold" do
+
+      let(:annotations) do
+        [Sequence.new(:sequence => 'AAANNNNTTT')]
+      end
+
+      it "should return fasta output of the contig" do
+        subject.run.should == ">contig00001\nAAA\n>contig00002\nTTT\n"
+      end
+
+    end
+
+  end
+
+end

data/spec/genomer-view-plugin/gff_record_helper_spec.rb

@@ -0,0 +1,244 @@
+require 'spec_helper'
+require 'genomer-plugin-view/gff_record_helper'
+
+describe GenomerPluginView::GffRecordHelper do
+
+  describe "module" do
+    it "should be included in Bio::GFF::GFF3::Record" do
+      Bio::GFF::GFF3::Record.ancestors.should include(described_class)
+    end
+  end
+
+  describe "#negative_strand?" do
+
+    subject do
+      Annotation.new
+    end
+
+    it "should return false for a positive strand annotation" do
+      subject.strand('+').to_gff3_record.
+        negative_strand?.should be_false
+    end
+
+    it "should return true for a negative strand annotation" do
+      subject.strand('-').to_gff3_record.
+        negative_strand?.should be_true
+    end
+
+  end
+
+  describe "#to_genbank_table_entry" do
+
+    before(:each) do
+      @attn = Annotation.new(:start => 1, :end => 3, :strand => '+',:feature => 'gene')
+    end
+
+    subject do
+      annotation.to_gff3_record.to_genbank_table_entry
+    end
+
+    context "gene feature on the positive strand" do
+
+      let(:annotation) do
+        @attn
+      end
+
+      it "should return a table entry" do
+        subject.should == <<-EOS.unindent
+        1\t3\tgene
+        EOS
+      end
+
+    end
+
+    context "gene feature on the negative strand" do
+
+      let(:annotation) do
+        @attn.strand('-')
+      end
+
+      it "should return a table entry" do
+        subject.should == <<-EOS.unindent
+        3\t1\tgene
+        EOS
+      end
+
+    end
+
+    context "gene feature with attributes" do
+
+      let(:annotation) do
+        @attn.feature('gene').attributes('ID' => 'id')
+      end
+
+      it "should return a table entry" do
+        subject.should == <<-EOS.unindent
+        1\t3\tgene
+        \t\t\tlocus_tag\tid
+        EOS
+      end
+
+    end
+
+    context "CDS feature on the positive strand" do
+
+      let(:annotation) do
+        @attn.feature('CDS')
+      end
+
+      it "should return a CDS table entry" do
+        subject.should == <<-EOS.unindent
+        1\t3\tCDS
+        EOS
+      end
+
+    end
+
+    context "tRNA feature on the positive strand" do
+
+      let(:annotation) do
+        @attn.feature('tRNA')
+      end
+
+      it "should return a CDS table entry" do
+        subject.should == <<-EOS.unindent
+        1\t3\ttRNA
+        EOS
+      end
+
+    end
+
+    context "tmRNA feature on the positive strand" do
+
+      let(:annotation) do
+        @attn.feature('tmRNA')
+      end
+
+      it "should return a CDS table entry" do
+        subject.should == <<-EOS.unindent
+        1\t3\ttmRNA
+        EOS
+      end
+
+    end
+
+    context "rRNA feature on the positive strand" do
+
+      let(:annotation) do
+        @attn.feature('rRNA')
+      end
+
+      it "should return a CDS table entry" do
+        subject.should == <<-EOS.unindent
+        1\t3\trRNA
+        EOS
+      end
+
+    end
+
+    context "miscRNA feature on the positive strand" do
+
+      let(:annotation) do
+        @attn.feature('miscRNA')
+      end
+
+      it "should return a CDS table entry" do
+        subject.should == <<-EOS.unindent
+        1\t3\tmiscRNA
+        EOS
+      end
+
+    end
+
+  end
+
+  describe "#table_attributes" do
+
+    before(:each) do
+      @attn = Annotation.new(:start => 1, :end => 3, :strand => '+', :feature => 'gene')
+    end
+
+    subject do
+      annotation.to_gff3_record.table_attributes
+    end
+
+    context "for an unknown feature type" do
+
+      let(:annotation) do
+        @attn.feature('unknown')
+      end
+
+      it "should raise an error" do
+        lambda{ subject.call }.should raise_error(Genomer::Error,"Unknown feature type 'unknown'")
+      end
+
+    end
+
+    context "for a feature with no attributes" do
+
+      let(:annotation) do
+        @attn
+      end
+
+      it "should return an empty array" do
+        subject.should be_empty
+      end
+
+    end
+
+    context "for a feature with an unknown attribute" do
+
+      let(:annotation) do
+        @attn.attributes('something' => 'else')
+      end
+
+      it "should return an empty array" do
+        subject.should be_empty
+      end
+
+    end
+
+    feature_keys = {
+      :gene => {
+        'Name' => 'gene',
+        'ID'   => 'locus_tag' },
+      :tRNA => {
+        'product' => 'product',
+        'Note'    => 'note'},
+      :rRNA => {
+        'product' => 'product',
+        'Note'    => 'note'},
+      :miscRNA => {
+        'product' => 'product',
+        'Note'    => 'note'},
+      :tmRNA => {
+        'product' => 'product',
+        'Note'    => 'note'},
+      :CDS  => {
+        'ec_number' => 'EC_number',
+        'function'  => 'function',
+        'product'   => 'product',
+        'Note'      => 'note',
+        'ID'        => 'protein_id' }}
+
+    feature_keys.each do |type,mappings|
+      mappings.each do |a,b|
+        context "#{type.to_s} feature" do
+
+          let(:annotation) do
+            @attn.feature(type.to_s).attributes(a => :value)
+          end
+
+          it "should return #{b} for the attribute #{a}" do
+            subject.first.should_not be_nil
+            subject.first.first.should == b
+          end
+
+        end
+      end
+    end
+
+
+  end
+
+end

data/spec/genomer-view-plugin/mapping_spec.rb

@@ -0,0 +1,89 @@
+require 'spec_helper'
+require 'genomer-plugin-view/mapping'
+
+describe GenomerPluginView::Mapping do
+
+  describe "#run" do
+
+    let(:annotations) do
+      [
+        gene(:start => 1,  :end => 3,  :attributes => {'ID' => 'gene1'}),
+        gene(:start => 4,  :end => 6,  :attributes => {'ID' => 'gene2'}),
+        gene(:start => 7,  :end => 9,  :attributes => {'ID' => 'gene3'}),
+        gene(:start => 10, :end => 12, :attributes => {'ID' => 'gene4'})
+      ]
+    end
+
+    before(:each) do
+      stub(Scaffolder::AnnotationLocator).new do
+        annotations
+      end
+      stub(subject).flags do
+        flags
+      end
+    end
+
+    subject do
+      described_class.new([],{})
+    end
+
+    describe "with no annotations or flags" do
+
+      let(:flags){ {} }
+
+      let(:annotations){ [] }
+
+      it "should return an empty mapping" do
+        subject.run.should == ""
+      end
+
+    end
+
+    describe "with some annotations" do
+
+      let(:flags){ {} }
+
+      it "should return a mapping of the same ids" do
+        subject.run.should == <<-EOS.unindent.strip
+        gene1\tgene1
+        gene2\tgene2
+        gene3\tgene3
+        gene4\tgene4
+        EOS
+      end
+
+    end
+
+    describe "with the prefix flag" do
+
+      let(:flags){ {:prefix => 'pre_'} }
+
+      it "should return a mapping to the prefixed ids" do
+        subject.run.should == <<-EOS.unindent.strip
+        gene1\tpre_gene1
+        gene2\tpre_gene2
+        gene3\tpre_gene3
+        gene4\tpre_gene4
+        EOS
+      end
+
+    end
+
+    describe "with the reset_locus_numbering flag " do
+
+      let(:flags){ {:reset_locus_numbering => true} }
+
+      it "should return a mapping to the reset ids" do
+        subject.run.should == <<-EOS.unindent.strip
+        gene1\t000001
+        gene2\t000002
+        gene3\t000003
+        gene4\t000004
+        EOS
+      end
+
+    end
+
+  end
+
+end