transrate 0.3.1 → 1.0.0.alpha.1

data/lib/transrate/bowtie2.rb

@@ -1,75 +0,0 @@
-module Transrate
-
-  class Bowtie2Error < StandardError
-  end
-
-  class Bowtie2
-
-    require 'which'
-    include Which
-
-    attr_reader :index_name, :sam
-
-    def initialize
-      bowtie2_path = which('bowtie2')
-      if bowtie2_path.empty?
-        raise Bowtie2Error.new("could not find bowtie2 in the path")
-      end
-      @bowtie2 = bowtie2_path.first
-      bowtie2_build_path = which('bowtie2-build')
-      if bowtie2_build_path.empty?
-        raise Bowtie2Error.new("could not find bowtie2-build in the path")
-      end
-      @bowtie2_build = bowtie2_build_path.first
-      @index_built = false
-      @index_name = ""
-    end
-
-    def map_reads(file, left,
-                  right, insertsize: 200,
-                  insertsd: 50, outputname: nil,
-                  threads: 8)
-      raise Bowtie2Error.new("Index not built") if !@index_built
-      lbase = File.basename(left)
-      rbase = File.basename(right)
-      index = File.basename(@index_name)
-      @sam = File.expand_path("#{lbase}.#{rbase}.#{index}.sam")
-      realistic_dist = insertsize + (3 * insertsd)
-      unless File.exists? @sam
-        # construct bowtie command
-        bowtiecmd = "#{@bowtie2} --very-sensitive"
-        bowtiecmd += " -p #{threads} -X #{realistic_dist}"
-        bowtiecmd += " --quiet --no-unal"
-        bowtiecmd += " --seed 1337"
-        bowtiecmd += " -x #{@index_name}"
-        bowtiecmd += " -1 #{left}"
-        # paired end?
-        bowtiecmd += " -2 #{right}" if right
-        bowtiecmd += " -S #{@sam}"
-        # run bowtie
-        runner = Cmd.new bowtiecmd
-        runner.run
-        if !runner.status.success?
-          raise Bowtie2Error.new("Bowtie2 failed\n#{runner.stderr}")
-        end
-      end
-      @sam
-    end
-
-    def build_index file
-      @index_name = File.basename(file).split(".")[0..-2].join(".")
-      unless File.exists?(@index_name + '.1.bt2')
-        cmd = "#{@bowtie2_build} --quiet --offrate 1 #{file} #{@index_name}"
-        runner = Cmd.new cmd
-        runner.run
-        if !runner.status.success?
-          msg = "Failed to build Bowtie2 index\n#{runner.stderr}"
-          raise Bowtie2Error.new(msg)
-        end
-      end
-      @index_built = true
-    end
-
-  end # Bowtie2
-
-end # Transrate

data/lib/transrate/dimension_reduce.rb

@@ -1,18 +0,0 @@
-module Transrate
-
-  class DimensionReduce
-
-    def self.dimension_reduce(metrics)
-      total = 0
-      metrics.each do |metric|
-        o = metric.origin
-        w = metric.weighting
-        a = metric.score
-        total += w * ((o - a) ** 2)
-      end
-      Math.sqrt(total) / metrics.length
-    end
-      
-  end # DimensionReduce
-
-end # Transrate

data/lib/transrate/metric.rb

@@ -1,16 +0,0 @@
-module Transrate
-
-  class Metric
-
-    attr_reader :origin, :score, :name, :weighting
-    
-    def initialize(name, score, origin)
-      @origin = origin
-      @score = score ? score : (1 - origin)
-      @name = name
-      @weighting = 1
-    end
-
-  end # Metric
-
-end # Transrate

data/test/test_bowtie.rb

@@ -1,66 +0,0 @@
-#!/usr/bin/env	ruby
-
-require 'helper'
-require 'tmpdir'
-
-class TestBowtie < Test::Unit::TestCase
-
-  context "bowtie" do
-
-    setup do
-      @reference = File.join(File.dirname(__FILE__), 'data',
-       'sorghum_transcript.fa')
-      @left = File.join(File.dirname(__FILE__), 'data', '150uncovered.l.fq')
-      @right = File.join(File.dirname(__FILE__), 'data', '150uncovered.r.fq')
-      @mapper = Transrate::Bowtie2.new
-    end
-
-    should "build index" do
-      Dir.mktmpdir do |tmpdir|
-        Dir.chdir tmpdir do
-          @mapper.build_index @reference
-          assert File.exist?("sorghum_transcript.1.bt2")
-        end
-      end
-    end
-
-    should "build index and map reads" do
-      Dir.mktmpdir do |tmpdir|
-        Dir.chdir tmpdir do
-          @mapper.build_index @reference
-          left = File.basename(@left)
-          right = File.basename(@right)
-          index = File.basename(@mapper.index_name)
-          @mapper.map_reads(@reference, @left, @right)
-          sam = @mapper.sam
-          assert File.exist?("#{sam}"), "sam file doesn't exist"
-          cmd = "grep -v \"^@\" #{sam} | wc -l "
-          line_in_sam_file = `#{cmd}`.chomp.to_i
-          assert_equal 424, line_in_sam_file
-        end
-      end
-    end
-
-    should "raise error when no index built" do
-      Dir.mktmpdir do |tmpdir|
-        Dir.chdir tmpdir do
-          assert_raise Transrate::Bowtie2Error do
-            @mapper.map_reads(@reference, @left, @right)
-          end
-        end
-      end
-    end
-
-    should "raise error when bowtie fails" do
-      not_reads = File.join(File.dirname(__FILE__), 'data', 'not_a_file.fq')
-      Dir.mktmpdir do |tmpdir|
-        Dir.chdir tmpdir do
-          assert_raise Transrate::Bowtie2Error do
-            @mapper.build_index @reference
-            @mapper.map_reads(@reference, @left, not_reads)
-          end
-        end
-      end
-    end
-  end
-end