transrate 1.0.0.alpha.8.bowtie → 1.0.0.beta1

data/lib/transrate/bowtie.rb

@@ -1,103 +0,0 @@
-module Transrate
-
-  class Bowtie2Error < StandardError
-  end
-
-  class Bowtie2
-
-    attr_reader :index_name, :sam, :read_count
-
-    def initialize
-      @bowtie2 = get_bin_path("bowtie2")
-      @bowtie2_build = get_bin_path("bowtie2-build")
-
-      @index_built = false
-      @index_name = ""
-    end
-
-    def get_bin_path bin
-      which_bin = Cmd.new("which #{bin}")
-      which_bin.run
-      if !which_bin.status.success?
-        raise IOError.new("ReadMetrics: could not find #{bin} in path")
-      end
-      which_bin.stdout.split("\n").first
-    end
-
-    def map_reads(file, left, right,
-                  insertsize: 200, insertsd: 50, threads: 8)
-      raise Bowtie2Error.new("Index not built") if !@index_built
-      lbase = File.basename(left.split(",").first)
-      rbase = File.basename(right.split(",").first)
-      index = File.basename(@index_name)
-      @sam = File.expand_path("#{lbase}.#{rbase}.#{index}.sam")
-      realistic_dist = insertsize + (5 * insertsd)
-      unless File.exists? @sam
-        # construct bowtie command
-        bowtiecmd = "#{@bowtie2} --very-sensitive"
-        bowtiecmd << " -x #{@index_name}"
-        bowtiecmd << " -a"
-        bowtiecmd << " -p #{threads} -X #{realistic_dist}"
-        bowtiecmd << " --no-unal"
-        bowtiecmd << " --seed 1337"
-        bowtiecmd << " --rdg 6,5"
-        bowtiecmd << " --rfg 6,5"
-        bowtiecmd << " --score-min L,-.6,-.4"
-        bowtiecmd << " -1 #{left}"
-        # paired end?
-        bowtiecmd << " -2 #{right}" if right
-        bowtiecmd << " -S #{@sam}"
-        # run bowtie
-        runner = Cmd.new bowtiecmd
-        runner.run
-        # parse bowtie output
-        if runner.stderr=~/([0-9]+)\ reads\;\ of\ these\:/
-          @read_count = $1.to_i
-          # save read_count to file
-          File.open("#{@sam}-read_count.txt", "wb") do |out|
-            out.write("#{@read_count}\n")
-          end
-        end
-        if !runner.status.success?
-          raise Bowtie2Error.new("Bowtie2 failed\n#{runner.stderr}")
-        end
-      else
-        @read_count = 0
-        if File.exist?("#{@sam}-read_count.txt")
-          @read_count = File.open("#{@sam}-read_count.txt").readlines.join.to_i
-        else
-          left.split(",").each do |l|
-            cmd = "wc -l #{l}"
-            count = Cmd.new(cmd)
-            count.run
-            if count.status.success?
-              @read_count += count.stdout.strip.split(/\s+/).first.to_i/4
-              File.open("#{@sam}-read_count.txt", "wb") do |out|
-                out.write("#{@read_count}\n")
-              end
-            else
-              logger.warn "couldn't get number of reads from #{l}"
-            end
-          end
-        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