ngs-ci 0.0.1.a

data/spec/lib/bin_spec.rb

@@ -0,0 +1,51 @@
+require 'spec_helper'
+
+testfasta="spec/test_files/test.fa"
+testbam="spec/test_files/test.bam"
+
+describe "bin executable" do
+
+  it "runs the --help option" do
+    c=NGSCI::Cmd.new("bundle exec bin/ngs-ci --help")
+    c.run
+    expect(c.stdout).to match /DESCRIPTION/
+    expect(c.status).to be_success
+  end
+  context "non-existent input files" do
+    it "fails on a non-existent bam file" do
+      c=NGSCI::Cmd.new("bundle exec bin/ngs-ci --bam foo.bam --reference #{testfasta}")
+      c.run
+      expect(c.status).to_not be_success
+    end
+
+    it "fails on a non-existent fasta file" do
+      c=NGSCI::Cmd.new("bundle exec bin/ngs-ci --bam #{testbam} --reference foo.fasta")
+      c.run
+      expect(c.status).to_not be_success
+    end
+  end
+  context "improper options" do
+    it "fails on improper strand-specific argument" do
+      c=NGSCI::Cmd.new("bundle exec bin/ngs-ci --bam #{testbam} --reference #{testfasta} --strand G")
+      c.run
+      expect(c.status).to_not be_success
+    end
+    it "fails on improper loglevel argument" do
+      c=NGSCI::Cmd.new("bundle exec bin/ngs-ci --bam #{testbam} --reference #{testfasta} --loglevel foo")
+      c.run
+      expect(c.status).to_not be_success
+    end    
+  end
+  it "runs on test data" do
+    c=NGSCI::Cmd.new("bundle exec bin/ngs-ci --bam #{testbam} --reference #{testfasta} --strand F")
+    c.run
+    expect(c.status).to be_success
+  end
+
+  it "produces speed information" do
+    c=NGSCI::Cmd.new("bundle exec bin/ngs-ci --bam #{testbam} --reference #{testfasta} --loglevel debug")
+    c.run
+    expect(c.stdout).to include("Measure Mode:")
+    
+  end
+end

data/spec/lib/calculator_spec.rb

@@ -0,0 +1,316 @@
+require 'spec_helper'
+require 'bio-samtools'
+
+testbam="spec/test_files/test.bam"
+emptybam="spec/test_files/empty.bam"
+testfasta="spec/test_files/test.fa"
+testout="spec/test_files/testfile.txt"
+
+
+
+describe "#run" do
+  context "during a strand specific run" do
+    before(:each) do
+      @calc=NGSCI::Calculator.new(testbam,testfasta,strand:"FR")
+      @testchrom=@calc.chroms.keys[0]
+    end
+    it "returns a hash" do
+      expect(@calc.run(runtime: false)).to be_instance_of Hash
+    end
+    it "returns the hash with keys of the chromosomes names" do
+      expect(@calc.run.keys).to eq(@calc.chroms.keys)
+    end
+    it "returns the hash with keys for each strand" do
+      expect(@calc.run[@testchrom].keys).to eq(%w(+ -))
+    end
+    it "returns NGSCI for each base of the genome" do
+      expect(@calc.run[@testchrom]["+"].size).to eq(@calc.chroms[@testchrom])
+    end
+  end
+
+  context "during an unstranded run" do
+    before(:each) do
+      @calc=NGSCI::Calculator.new(testbam,testfasta)
+      @testchrom=@calc.chroms.keys[0]
+    end
+    it "returns the hash with keys of the chromosomes names" do
+      expect(@calc.run.keys).to eq(@calc.chroms.keys)
+    end
+    it "returns the hash with a nil strand key" do
+      expect(@calc.run[@testchrom].keys[0]).to be nil
+    end
+    it "returns NGSCI for each base of the genome" do
+      expect(@calc.run[@testchrom][nil].size).to eq(@calc.chroms[@testchrom])
+    end
+  end
+end
+
+describe "#readblock" do
+  context "when reading the first block" do
+    it "returns a hash with an array of length @block_size" do
+      @calc=NGSCI::Calculator.new(testbam,testfasta)
+      results=@calc.readblock(@calc.chroms.keys[0],0)
+      result_length=results[results.keys[0]].size
+      expect(result_length).to eq(@calc.block_size)
+    end
+  end
+  context "when reading any other block" do
+    it "returns a hash with and array of length @block_size" do
+      @calc=NGSCI::Calculator.new(testbam,testfasta)
+      results=@calc.readblock(@calc.chroms.keys[0],1)
+      result_length=results[results.keys[0]].size
+      expect(result_length).to eq(@calc.block_size)      
+    end
+  end
+end
+
+describe "#sci" do
+  context "when passed an array of read objects" do
+    before(:each) do
+      @calc = NGSCI::Calculator.new(testbam,testfasta)
+      @bam = Bio::DB::Sam.new(:bam=>testbam,:fasta=>testfasta)
+      @bam.open
+      @reads = []
+      @bam.fetch("NC_001988.2",75,75){|x| read = @calc.convert(x); @reads << read unless read.nil?}
+      @reads = @reads.uniq{|r|r.start}
+    end
+    it "returns an array" do
+      expect(@calc.sci(@reads)).to be_kind_of(Array)
+    end
+    it "returns the sequencing complexity index" do
+      expect(@calc.sci(@reads)[-1]).to eq(0.0)
+    end
+  end
+  context "when passed an empty array" do
+    it "returns nil" do
+      @calc = NGSCI::Calculator.new(testbam,testfasta)
+      empty_sci = @calc.sci([])[-1]
+      expect(empty_sci).to be_zero
+    end
+  end
+end
+
+describe "#read_length" do
+  it "calculates the read length" do
+    @calc=NGSCI::Calculator.new(testbam,testfasta)
+    expect(@calc.buffer).to eq(76)
+  end
+  it "fails on an empty bam file" do
+    expect{NGSCI::Calculator.new(emptybam,testfasta)}.to raise_error(NGSCI::NGSCIIOError)
+    `rm #{emptybam}.bai`
+  end
+end
+
+describe "#summed_overlaps" do
+  it "returns an int" do
+    @bam=Bio::DB::Sam.new(:bam=>testbam,:fasta=>testfasta)
+    @bam.open
+    @reads = []
+    @calc=NGSCI::Calculator.new(testbam,testfasta)
+    @bam.fetch("NC_001988.2",8,75) {|x| read=@calc.convert(x); @reads << read if read}
+    @reads = @reads.uniq{|r| r.start}
+    expect(@calc.summed_overlaps(@reads)).to be_an(Integer)
+  end
+  context "when passed an array of read objects" do
+    before(:each) do
+      @bam=Bio::DB::Sam.new(:bam=>testbam,:fasta=>testfasta)
+      @bam.open
+      @reads = []
+      @calc=NGSCI::Calculator.new(testbam,testfasta)
+      @bam.fetch("NC_001988.2",8,75) {|x| read=@calc.convert(x); @reads << read if read}
+      @reads = @reads.uniq{|r| r.start}
+    end
+    it "returns the #overlap of two reads" do
+      summed_overlap = 2*@calc.overlap(@reads[0],@reads[1])
+      expect(@calc.summed_overlaps(@reads[0..1])).to eq(summed_overlap)
+    end
+
+    it "calculates the average overlap between a group of reads" do
+      expect(@calc.summed_overlaps(@reads[0..7]).round(4)).to eq(380.0)
+    end
+  end
+  context "when passed an array with a single read object" do
+    it "returns zero" do
+      @bam=Bio::DB::Sam.new(:bam=>testbam,:fasta=>testfasta)
+      @bam.open
+      @reads=[]
+      @calc=NGSCI::Calculator.new(testbam,testfasta)
+      @bam.fetch("NC_001988.2",8,75) {|x| read=@calc.convert(x); @reads << read if read}
+      expect(@calc.summed_overlaps([@reads[0]])).to be_zero
+    end
+  end
+  context "when passed an empty array" do
+    it "returns zero" do
+      @calc=NGSCI::Calculator.new(testbam,testfasta)
+      expect(@calc.summed_overlaps([])).to be_zero
+    end
+  end
+end
+
+describe "#overlap" do
+  before(:each) do
+    @bam=Bio::DB::Sam.new(:bam=>testbam,:fasta=>testfasta)
+    @bam.open
+    @reads=[]
+    @bam.fetch("NC_001988.2",0,200) {|x| @reads << x}
+    @calc=NGSCI::Calculator.new(testbam,testfasta)
+    @read1=@calc.convert(@reads[2])
+    @read2=@calc.convert(@reads[3])
+  end
+  it "calculates the overlap between two reads" do
+    expect(@calc.overlap(@read1,@read2)).to eq(14)
+  end
+
+  it "calculates the overlap regardless of order" do
+    expect(@calc.overlap(@read2,@read1)).to eq(14)
+  end
+end
+
+describe '#reference_sequences' do
+  before(:each) do
+    @calc=NGSCI::Calculator.new(testbam,testfasta)
+  end
+
+  it "retrieves reference sequences" do
+    expect(@calc.reference_sequences(testfasta).keys).to include "NC_001988.2"
+  end
+end
+
+describe '#newread' do
+  before(:each) do
+    @bam=Bio::DB::Sam.new(:bam=>testbam,:fasta=>testfasta)
+    @bam.open
+    @reads=[]
+    @bam.fetch("NC_001988.2",0,200) {|x| @reads << x}
+    @calc=NGSCI::Calculator.new(testbam,testfasta)
+  end
+
+  it "converts an alignment object to a read object" do
+    expect(@calc.newread(@reads[0])).to be_instance_of NGSCI::Read
+  end  
+end
+
+describe "#fr" do
+  before(:each) do
+    @bam=Bio::DB::Sam.new(:bam=>testbam,:fasta=>testfasta)
+    @bam.open
+    @reads=[]
+    @bam.fetch("NC_001988.2",0,200) {|x| @reads << x}
+    @calc=NGSCI::Calculator.new(testbam,testfasta)
+    @testpair=[@reads[5],@reads[10]]
+  end
+
+  it "converts the first read with FR chemistry" do
+    first=@calc.fr(@testpair[0])
+    expect(first.strand).to eq("+")
+  end
+  it "converts the second read with FR chemistry" do
+    second=@calc.fr(@testpair[1])
+    expect(second.strand).to eq("+")
+  end
+end
+
+describe "#rf" do
+  before(:each) do
+    @bam=Bio::DB::Sam.new(:bam=>testbam,:fasta=>testfasta)
+    @bam.open
+    @reads=[]
+    @bam.fetch("NC_001988.2",0,200) {|x| @reads << x}
+    @calc=NGSCI::Calculator.new(testbam,testfasta)
+    @testpair=[@reads[5],@reads[10]]
+  end
+  it "converts the first read with RF chemistry" do
+    first=@calc.rf(@testpair[0])
+    expect(first.strand).to eq("-")
+  end
+
+  it "converts the second read with RF chemistry" do
+    second=@calc.rf(@testpair[1])
+    expect(second.strand).to eq("-")
+  end
+end
+
+describe "#f" do
+  before(:each) do
+    @bam=Bio::DB::Sam.new(:bam=>testbam,:fasta=>testfasta)
+    @bam.open
+    @reads=[]
+    @bam.fetch("NC_001988.2",0,200) {|x| @reads << x}
+    @calc=NGSCI::Calculator.new(testbam,testfasta)
+    @testpair=[@reads[5],@reads[10]]
+  end
+  it "converts a read with F chemistry on the + strand" do
+    first=@calc.f(@testpair[0])
+    expect(first.strand).to eq("-")
+  end
+  it "converts a read with F chemistry on the - strand" do
+    second=@calc.f(@testpair[1])
+    expect(second.strand).to eq("+")
+  end
+
+end
+
+describe '#convert' do
+  before(:each) do
+    @bam=Bio::DB::Sam.new(:bam=>testbam,:fasta=>testfasta)
+    @bam.open
+    @reads=[]
+    @bam.fetch("NC_001988.2",0,200) {|x| @reads << x}
+  end
+  it "converts an alignment object to a read object" do
+    calc=NGSCI::Calculator.new(testbam,testfasta)
+    expect(calc.convert(@reads[2])).to be_instance_of NGSCI::Read
+  end
+
+  it "returns nil for an unmapped read" do
+    calc=NGSCI::Calculator.new(testbam,testfasta)
+    expect(calc.convert(@reads[1])).to be_nil
+  end
+
+  it "converts the first read in FR chemistry aligned to the + strand" do
+    calc=NGSCI::Calculator.new(testbam,testfasta,strand:"FR")
+    testpair=[@reads[5],@reads[10]]
+    first=calc.convert(testpair[1])
+    expect(first.strand).to eq("+")
+  end
+  it "converts the second read in FR chemistry aligned to the - strand" do
+    calc=NGSCI::Calculator.new(testbam,testfasta,strand:"FR")
+    testpair=[@reads[5],@reads[10]]
+    second=calc.convert(testpair[0])
+    expect(second.strand).to eq("+")
+  end
+  it "converts the first read in RF chemistry aligned to the + strand" do
+    calc=NGSCI::Calculator.new(testbam,testfasta,strand:"RF")
+    testpair=[@reads[5],@reads[10]]
+    first=calc.convert(testpair[1])
+    expect(first.strand).to eq("-")
+  end
+  it "converts the second read in FR chemistry aligned to the - strand" do
+    calc=NGSCI::Calculator.new(testbam,testfasta,strand:"RF")
+    testpair=[@reads[5],@reads[10]]
+    second=calc.convert(testpair[0])
+    expect(second.strand).to eq("-")
+  end
+
+end
+
+describe "#export" do
+  context "calculator has not run" do
+    it "returns nil" do
+      calc=NGSCI::Calculator.new(testbam,testfasta)
+      expect(calc.export(testout)).to be nil
+    end
+  end
+  context "calculator has run" do
+    after(:all) do
+      `rm #{testout}`
+    end
+    it "returns outfile" do
+      calc=NGSCI::Calculator.new(testbam,testfasta)
+      calc.run
+      expect(calc.export(testout)).to eq(testout)
+    end
+  end
+end
+
+

data/spec/lib/cmd_spec.rb

@@ -0,0 +1,17 @@
+require 'spec_helper'
+
+
+describe "command" do
+
+  it "runs commands" do
+    c=NGSCI::Cmd.new("echo success")
+    c.run
+    expect(c.stdout.chomp).to eq("success")
+  end
+
+  it "receives commands" do
+    c=NGSCI::Cmd.new("echo success")
+    expect(c.to_s).to eq("echo success")    
+  end
+
+end

data/spec/lib/read_spec.rb

@@ -0,0 +1,35 @@
+require 'spec_helper'
+
+
+describe "reads" do
+
+  it "fails to instantiate on a string start site" do
+    expect{NGSCI::Read.new("foo",3)}.to raise_error(NGSCI::NGSCIError)
+  end
+
+  it "fails to instantiate on a string stop site" do
+    expect{NGSCI::Read.new(1,"foo")}.to raise_error(NGSCI::NGSCIError)
+  end
+
+  it "fails to instantiate when the stop site is greater than the start site" do
+    expect{NGSCI::Read.new(3,1)}.to raise_error(NGSCI::NGSCIError)
+  end
+
+  it "fails to instantiate on an improper strand argument" do
+    expect{NGSCI::Read.new(1,3,strand:"foo")}.to raise_error(NGSCI::NGSCIError)
+  end
+
+  it "fails to instantiate without the three necessary arguments" do
+    expect{NGSCI::Read.new(1)}.to raise_error(ArgumentError)
+  end
+
+  it "instantiates a new read with proper unstranded arguments" do
+    expect{NGSCI::Read.new(1,3)}.to_not raise_error
+  end
+
+  it "instantiates a new read with proper stranded arguments" do
+    expect{NGSCI::Read.new(1,3,strand:"+")}.to_not raise_error
+  end
+
+
+end

data/spec/spec_helper.rb

@@ -0,0 +1,11 @@
+require 'coveralls'
+Coveralls.wear!
+
+require 'NGSCI'
+
+
+RSpec.configure do |config|
+
+  config.color=true
+
+end