big_simon.rb in big_simon-0.1.0

- old
+ new
@@ -1,100 +1,27 @@
 require "rya"
+require "set"
+require "pp"
 
 require "big_simon/version"
 
+require "big_simon/utils"
+
+require "big_simon/runners"
+require "big_simon/parsers"
+require "big_simon/pipeline"
+
 Time.extend Rya::CoreExtensions::Time
 Process.extend Rya::CoreExtensions::Process
+Array.include Rya::CoreExtensions::Array
+Math.extend Rya::CoreExtensions::Math
 
 module BigSimon
-
-  # Project directories
   ROOT       = File.join __dir__, ".."
   BIN        = File.join ROOT, "vendor", "bin", "mac"
   SPEC       = File.join ROOT, "spec"
   TEST_FILES = File.join SPEC, "test_files"
-
-  class Parsers
-
-    def self.vir_host_matcher fname
-      hosts = nil
-
-      host_info = {}
-      File.open(fname, "rt").each_line.with_index do |line, idx|
-        line.chomp!
-        line.sub! /,$/, "" # git rid of trailing commas
-
-        if idx.zero?
-          stat, *hosts = line.split ","
-        else
-          ary   = line.split ","
-          virus = ary.shift
-
-          dists = ary.map.
-              with_index { |dist, idx| [hosts[idx], dist.to_f] }.
-              sort_by { |_, dist| dist }
-
-          best_host = dists[0][0]
-
-          host_info[virus] = {
-              best: best_host,
-              all:  dists
-          }
-        end
-      end
-
-      host_info
-    end
-  end
-
-  class Runners
-
-    # Runs the WIsH program
-    #
-    # @raise [AbortIf::Exit] if commands fail
-    def self.wish exe, vir_dir, host_dir, outdir, threads
-      model_dir = File.join outdir, "model"
-
-      FileUtils.mkdir_p model_dir
-
-      build_model = "#{exe} " \
-      "-t #{threads} " \
-      "-c build " \
-      "-g #{host_dir} " \
-      "-m #{model_dir}"
-
-      predict = "#{exe} " \
-      "-t #{threads} " \
-      "-c predict " \
-      "-g #{vir_dir} " \
-      "-m #{model_dir} " \
-      "-r #{outdir} -b"
-
-      Process.run_and_time_it! "Building model", build_model
-      Process.run_and_time_it! "Predicting host", predict
-
-      FileUtils.rm_r model_dir if Dir.exist? model_dir
-    end
-
-    def self.vir_host_matcher exe, vir_dir, host_dir, outdir
-      FileUtils.mkdir_p outdir
-
-      cmd = "python #{exe} " \
-      "-v #{vir_dir} " \
-      "-b #{host_dir} " \
-      "-o #{outdir} " \
-      "-d 1" # only compute d2star dissimilarity
-
-      Process.run_and_time_it! "Computing d2star dissimilarity", cmd
-
-      tmp_dir = File.join outdir, "tmp"
-      FileUtils.rm_r tmp_dir if Dir.exist? tmp_dir
-
-      bad_files = %w[d2star_k6_main.html hostTaxa.txt_new.txt]
-      bad_files.each do |fname|
-        path = File.join outdir, fname
-
-        FileUtils.rm path if File.exist? path
-      end
-    end
-  end
+  WISH       = File.join BIN, "WIsH"
+  VHM        = File.join BIN, "vhm.py"
+  MUMMER     = File.join BIN, "mummer"
+  RSCRIPT = "Rscript"
 end