From 37c181c7d7f521fed243bbc0121d3f13ce563389 Mon Sep 17 00:00:00 2001
From: Chris Boursnell <cmb211@cam.ac.uk>
Date: Thu, 19 Dec 2013 13:07:30 +0000
Subject: [PATCH 01/14] fixes to loading config file and a few other little
 things

---
 .gitignore                                    |  2 ++
 Gemfile.lock                                  |  4 +--
 assemblotron.gemspec                          |  2 +-
 lib/assemblotron.rb                           |  4 ++-
 .../assemblers/soap_denovo_trans.rb           | 28 +++++++++++++++----
 .../assemblers/soap_denovo_trans.yml          |  2 +-
 6 files changed, 31 insertions(+), 11 deletions(-)

diff --git a/.gitignore b/.gitignore
index ec5e31a..b38f55a 100644
--- a/.gitignore
+++ b/.gitignore
@@ -11,6 +11,8 @@ spec/reports
 test/tmp
 test/version_tmp
 tmp
+*~
+*fastq
 
 # YARD artifacts
 .yardoc
diff --git a/Gemfile.lock b/Gemfile.lock
index 0d3c00d..7af27b6 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -4,7 +4,7 @@ PATH
     assemblotron (0.0.1)
       biopsy (= 0.1.6.alpha)
       rake (~> 10.1.0)
-      transrate (= 0.0.9)
+      transrate (= 0.0.11)
       trollop (~> 2.0)
 
 GEM
@@ -83,7 +83,7 @@ GEM
     thor (0.18.1)
     threach (0.2.0)
     tins (0.9.0)
-    transrate (0.0.9)
+    transrate (0.0.11)
       bettersam (~> 0.0.1.alpha)
       bio
       rake (~> 10.1.0)
diff --git a/assemblotron.gemspec b/assemblotron.gemspec
index 7ac14d1..f488768 100644
--- a/assemblotron.gemspec
+++ b/assemblotron.gemspec
@@ -16,7 +16,7 @@ Gem::Specification.new do |gem|
   gem.add_dependency 'rake', '~> 10.1.0'
   gem.add_dependency 'biopsy', '0.1.6.alpha'
   gem.add_dependency 'trollop', '~> 2.0'
-  gem.add_dependency 'transrate', '0.0.9'
+  gem.add_dependency 'transrate', '0.0.11'
 
   gem.add_development_dependency 'turn'
   gem.add_development_dependency 'simplecov'
diff --git a/lib/assemblotron.rb b/lib/assemblotron.rb
index 2dd76f3..91a264a 100644
--- a/lib/assemblotron.rb
+++ b/lib/assemblotron.rb
@@ -151,9 +151,11 @@ def self.class_from_type type
 
     def run assembler
       @assembler_opts[:reference] = Transrate::Assembly.new(@assembler_opts[:reference])
+      @assembler_opts[:left] = File.expand_path(@assembler_opts[:left])
+      @assembler_opts[:right] = File.expand_path(@assembler_opts[:right])
       a = self.get_assembler assembler
       e = Biopsy::Experiment.new a, @assembler_opts
-      res = e.run
+      @res = e.run
     end # run
 
   end # Controller
diff --git a/lib/assemblotron/assemblers/soap_denovo_trans.rb b/lib/assemblotron/assemblers/soap_denovo_trans.rb
index 634a7fa..2291b4b 100644
--- a/lib/assemblotron/assemblers/soap_denovo_trans.rb
+++ b/lib/assemblotron/assemblers/soap_denovo_trans.rb
@@ -13,16 +13,32 @@ def initialize
 
   def run params
     # run the assembly
+    self.setup_soap params
     self.run_soap params
     # retrieve output
     scaffolds = Dir['*.scafSeq']
-    return nil if scaffolds.empty?
-    puts scaffolds
+    return nil if scaffolds.empty? 
+    # puts scaffolds
     scaffolds = scaffolds.first 
     # return a Transrater
     Transrate::Transrater.new(scaffolds, params[:reference], params[:left], params[:right])
   end
 
+  # soapdt.config file only generated on first run
+  def setup_soap params
+    # make config file
+    File.open("soapdt.config", "w") do |conf|
+      conf.puts "max_rd_len=20000"
+      conf.puts "[LIB]"
+      conf.puts "avg_ins=#{params[:insertsize]}"
+      conf.puts "reverse_seq=0"
+      conf.puts "asm_flags=3"
+      conf.puts "rank=2"
+      conf.puts "q1=#{params[:left]}"
+      conf.puts "q2=#{params[:right]}"
+    end
+  end
+
   def include_defaults params
     defaults = {
       :K => 23,
@@ -36,16 +52,16 @@ def include_defaults params
       :t => 5,
       :G => 50
     }
-    defaults.merge params
+    defaults.merge(params) { |key, v1, v2| v2 }
   end
 
   def construct_command(params)
     params = self.include_defaults params
     cmd = "#{@path} all"
     # generic
-    cmd += " -s #{params[:config]}" # config file
+    cmd += " -s soapdt.config" # config file
     cmd += " -a #{params[:memory]}" if params.has_key? :memory # memory assumption
-    cmd += " -o #{params[:out]}" if params.has_key? :out # output directory
+    cmd += " -o #{params[:out]}" if params.has_key? :out # output prefix
     cmd += " -p #{params[:threads]}" # number of threads
     # specific
     cmd += " -K #{params[:K]}" # kmer size
@@ -61,7 +77,7 @@ def construct_command(params)
   # runs SOAPdt script
   def run_soap(params)
     cmd = self.construct_command(params)
-    puts cmd
+    # puts cmd
     `#{cmd} > #{@count}.log`
   end
 
diff --git a/lib/assemblotron/assemblers/soap_denovo_trans.yml b/lib/assemblotron/assemblers/soap_denovo_trans.yml
index ddf1e5c..726f427 100644
--- a/lib/assemblotron/assemblers/soap_denovo_trans.yml
+++ b/lib/assemblotron/assemblers/soap_denovo_trans.yml
@@ -16,7 +16,7 @@ parameters:
   right:
     type: string
     opt: false
-    desc: 'Path to left reads (for assembly quality analysis)'
+    desc: 'Path to right reads (for assembly quality analysis)'
   insertsize:
     type: integer
     opt: false

From 95e2d61bc774b04bcbafc7fc70ad92ef36de2d1d Mon Sep 17 00:00:00 2001
From: Chris Boursnell <cboursnell@gmail.com>
Date: Tue, 22 Apr 2014 12:51:14 +0100
Subject: [PATCH 02/14] fixed soap denovo test

---
 .../assemblers/soap_denovo_trans.rb           | 28 ++++---------------
 test/test_soap_denovo_trans.rb                |  6 ++--
 2 files changed, 8 insertions(+), 26 deletions(-)

diff --git a/lib/assemblotron/assemblers/soap_denovo_trans.rb b/lib/assemblotron/assemblers/soap_denovo_trans.rb
index 6883e46..ef93437 100644
--- a/lib/assemblotron/assemblers/soap_denovo_trans.rb
+++ b/lib/assemblotron/assemblers/soap_denovo_trans.rb
@@ -8,12 +8,11 @@ def initialize
     @count = 0
     @path = which('SOAPdenovo-Trans-127mer')
     raise "SOAPdenovo-Trans-127mer was not in the PATH" if @path.empty?
-    @path = @path.first
+    @path = File.basename(@path.first)
   end
 
   def run params
     # run the assembly
-    self.setup_soap params
     self.run_soap params
     # retrieve output
     scaffolds = Dir['*.scafSeq']
@@ -25,26 +24,12 @@ def run params
     Transrate::ComparativeMetrics.new(assembly, params[:reference])
   end
 
-  # soapdt.config file only generated on first run
-  def setup_soap params
-    # make config file
-    File.open("soapdt.config", "w") do |conf|
-      conf.puts "max_rd_len=20000"
-      conf.puts "[LIB]"
-      conf.puts "avg_ins=#{params[:insertsize]}"
-      conf.puts "reverse_seq=0"
-      conf.puts "asm_flags=3"
-      conf.puts "rank=2"
-      conf.puts "q1=#{params[:left]}"
-      conf.puts "q2=#{params[:right]}"
-    end
-  end
-
   def include_defaults params
     defaults = {
       :K => 23,
       :threads => 8,
       :out => 'sdt',
+      :config => 'soapdt.config',
       :d => 0,
       :e => 2,
       :M => 1,
@@ -53,6 +38,7 @@ def include_defaults params
       :t => 5,
       :G => 50
     }
+    # params argument takes precedence over defaults in merge
     defaults.merge(params) { |key, v1, v2| v2 }
   end
 
@@ -60,9 +46,9 @@ def construct_command(params)
     params = self.include_defaults params
     cmd = "#{@path} all"
     # generic
-    cmd += " -s soapdt.config" # config file
+    cmd += " -s #{params[:config]}" # config file
     cmd += " -a #{params[:memory]}" if params.has_key? :memory # memory assumption
-    cmd += " -o #{params[:out]}" if params.has_key? :out # output prefix
+    cmd += " -o #{params[:out]}" if params.has_key? :out # output directory
     cmd += " -p #{params[:threads]}" # number of threads
     # specific
     cmd += " -K #{params[:K]}" # kmer size
@@ -78,10 +64,6 @@ def construct_command(params)
   # runs SOAPdt script
   def run_soap(params)
     cmd = self.construct_command(params)
-<<<<<<< HEAD
-    # puts cmd
-=======
->>>>>>> 94df5a6a0ea9a66d408007776166531628eab69d
     `#{cmd} > #{@count}.log`
   end
 
diff --git a/test/test_soap_denovo_trans.rb b/test/test_soap_denovo_trans.rb
index 4c727dc..88c6ede 100644
--- a/test/test_soap_denovo_trans.rb
+++ b/test/test_soap_denovo_trans.rb
@@ -15,7 +15,7 @@ class TestSoapDenovoTrans < Test::Unit::TestCase
         :insertsize => '200',
         :l => 'l.fq',
         :r => 'r.fq',
-        :path => 'SOAPdenovo-Trans',
+        :path => 'SOAPdenovo-Trans-127mer',
         :memory => 12,
         :threads => 8,
         :out => 1,
@@ -34,14 +34,14 @@ class TestSoapDenovoTrans < Test::Unit::TestCase
         :t => 6
       }
       @params.merge! params
-      expected = "SOAPdenovo-Trans all -s soapdt.config"
+      expected = "SOAPdenovo-Trans-127mer all -s soapdt.config"
       expected += " -a 12 -o 1 -p 8 -K 1 -d 2 -F -M 9 -L 200"
       expected += " -e 6 -t 6 -G 50"
       assert_equal expected, @s.construct_command(@params)
     end
 
     should "automatically include defaults" do
-      expected = "SOAPdenovo-Trans all -s soapdt.config"
+      expected = "SOAPdenovo-Trans-127mer all -s soapdt.config"
       expected += " -a 12 -o 1 -p 8 -K 23 -d 0 -F -M 1"
       expected += " -L 100 -e 2 -t 5 -G 50"
       assert_equal expected, @s.construct_command(@params)

From 2e14db0c6b293c97fef219c0a11548a4fb70b321 Mon Sep 17 00:00:00 2001
From: Chris Boursnell <cboursnell@gmail.com>
Date: Fri, 25 Apr 2014 12:55:47 +0100
Subject: [PATCH 03/14] optimiser and verbosity option

---
 bin/atron           |  5 ++++-
 lib/assemblotron.rb | 34 +++++++++++++++++++++++-----------
 2 files changed, 27 insertions(+), 12 deletions(-)

diff --git a/bin/atron b/bin/atron
index 7fb1daf..e01e509 100755
--- a/bin/atron
+++ b/bin/atron
@@ -35,10 +35,13 @@ EOS
   opt :gzip_intermediates, "gzip intermediate files (onlys takes effect if --keep-intermediates is on)"
   opt :skip_subsample, "skip subsampling step"
   opt :skip_final, "skip final assembly step"
+  opt :optimiser, "Which optimiser to use. Possible: 'tabu' or 'sweeper' (default:'tabu')", :type => String, 
+          :default => "tabu"
   opt :logfile, "write logs to file", :type => String
   opt :output_parameters, "file to which optimal parameters will be written", :default => "optimal_parameters.json"
   opt :quiet, "Don't print any logs"
-  opt :verbose, "Print extra information"
+  opt :verbosity, "How much extra information is printed [silent|quiet|loud]",
+          :type => String, :default => "silent"
   opt :visualise, "Produce visualisations of the run"
   stop_on SUB_COMMANDS
 end
diff --git a/lib/assemblotron.rb b/lib/assemblotron.rb
index 91470d8..3aa8837 100644
--- a/lib/assemblotron.rb
+++ b/lib/assemblotron.rb
@@ -111,7 +111,7 @@ def list_assemblers
     def options_for_assembler assembler
       a = self.get_assembler assembler
       parser = Trollop::Parser.new do
-          banner <<-EOS
+      banner <<-EOS
 #{Controller.header}
 
 Options for assembler #{assembler}
@@ -133,8 +133,7 @@ def options_for_assembler assembler
 
     def get_assembler assembler
       ret = @assemblers.find do |a|
-        a.name == assembler || 
-        a.shortname == assembler
+        a.name == assembler || a.shortname == assembler
       end
       raise "couldn't find assembler #{assembler}" if ret.nil?
       ret
@@ -185,14 +184,30 @@ def run assembler
       end
 
       # load reference and create ublast DB
-      @assembler_opts[:reference] = Transrate::Assembly.new(@assembler_opts[:reference])
-
-      ra = Transrate::ReciprocalAnnotation.new(@assembler_opts[:reference], @assembler_opts[:reference])
+      @assembler_opts[:reference] = 
+        Transrate::Assembly.new(@assembler_opts[:reference])
+      ra = Transrate::ReciprocalAnnotation.new(@assembler_opts[:reference],
+                                               @assembler_opts[:reference])
       ra.make_reference_db
 
       # run the assemblotron
       a = self.get_assembler assembler
-      e = Biopsy::Experiment.new a, @assembler_opts, @global_opts[:threads]
+      start = nil
+      algorithm = nil
+      if @global_opts[:optimiser] == 'tabu'
+        algorithm = Biopsy::TabuSearch.new(a.parameters)
+      elsif @global_opts[:optimiser] == 'sweeper'
+        algorithm = Biopsy::ParameterSweeper.new(a.parameters)
+      else
+        raise NotImplementedError, "please select either tabu or\                                                     
+         sweeper as the optimiser"
+      end
+
+      e = Biopsy::Experiment.new(a, @assembler_opts,
+                                 @global_opts[:threads],
+                                 start,
+                                 algorithm,
+                                 @global_opts[:verbosity].to_sym)
       res = e.run
 
       # write out the result
@@ -201,10 +216,7 @@ def run assembler
       end
 
       # run the final assembly
-      unless @global_opts[:skip_final]
-        final_assembly a, res
-      end
-
+      final_assembly a, res unless @global_opts[:skip_final]
     end # run
 
   end # Controller

From f4af09514c9381ba47b43ed7301a1f728bfa0b1c Mon Sep 17 00:00:00 2001
From: Chris Boursnell <cboursnell@gmail.com>
Date: Fri, 25 Apr 2014 14:29:19 +0100
Subject: [PATCH 04/14] enable writing when creating config file

---
 lib/assemblotron/assemblers/soap_denovo_trans.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/assemblotron/assemblers/soap_denovo_trans.rb b/lib/assemblotron/assemblers/soap_denovo_trans.rb
index 1942558..01697e2 100644
--- a/lib/assemblotron/assemblers/soap_denovo_trans.rb
+++ b/lib/assemblotron/assemblers/soap_denovo_trans.rb
@@ -98,7 +98,7 @@ def setup_full(global_opts, assembler_opts)
   def create_config left, right, assembler_opts
     # create the config file
     filename = "#{Time.now}.full.config"
-    File.open(filename) do |f|
+    File.open(filename,'w') do |f|
       f << 'max_rd_len=5000'
       f << '[LIB]'
       f << "avg_ins=#{assembler_opts[:insertsize]}"

From 517347c293838f26d11e29123632999d9d7d9b21 Mon Sep 17 00:00:00 2001
From: Chris Boursnell <cboursnell@gmail.com>
Date: Fri, 25 Apr 2014 14:31:56 +0100
Subject: [PATCH 05/14] changed spaces to underscores in the config file
 filename

---
 lib/assemblotron/assemblers/soap_denovo_trans.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/assemblotron/assemblers/soap_denovo_trans.rb b/lib/assemblotron/assemblers/soap_denovo_trans.rb
index 01697e2..2c88d52 100644
--- a/lib/assemblotron/assemblers/soap_denovo_trans.rb
+++ b/lib/assemblotron/assemblers/soap_denovo_trans.rb
@@ -97,7 +97,7 @@ def setup_full(global_opts, assembler_opts)
   # @return [String] full path to the generated config gile
   def create_config left, right, assembler_opts
     # create the config file
-    filename = "#{Time.now}.full.config"
+    filename = "#{Time.now}.full.config".tr(" ","_")
     File.open(filename,'w') do |f|
       f << 'max_rd_len=5000'
       f << '[LIB]'

From 8ce456bca6851817a1be0b6096b11748f09f118e Mon Sep 17 00:00:00 2001
From: Chris Boursnell <cboursnell@gmail.com>
Date: Fri, 25 Apr 2014 14:59:19 +0100
Subject: [PATCH 06/14] bump

---
 2014-04-25_14:31:11_+0100.full.config             |  1 +
 Gemfile.lock                                      | 15 ++++++++++-----
 assemblotron.gemspec                              |  4 ++--
 bin/atron                                         | 10 +++++-----
 lib/assemblotron.rb                               |  2 ++
 lib/assemblotron/assemblers/soap_denovo_trans.yml |  5 -----
 6 files changed, 20 insertions(+), 17 deletions(-)
 create mode 100644 2014-04-25_14:31:11_+0100.full.config

diff --git a/2014-04-25_14:31:11_+0100.full.config b/2014-04-25_14:31:11_+0100.full.config
new file mode 100644
index 0000000..71df0b0
--- /dev/null
+++ b/2014-04-25_14:31:11_+0100.full.config
@@ -0,0 +1 @@
+max_rd_len=5000[LIB]avg_ins=reverse_seq=0asm_flags=3q1=/home/chris/documents/subset.Cd.keep.1q2=/home/chris/documents/subset.Cd.keep.2
\ No newline at end of file
diff --git a/Gemfile.lock b/Gemfile.lock
index 952c075..410c04b 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -3,8 +3,8 @@ PATH
   specs:
     assemblotron (0.0.2)
       RubyInline (~> 3.12)
-      biopsy (= 0.1.8)
-      rake (~> 10.1)
+      biopsy (= 0.1.9)
+      rake (~> 10.3)
       transrate (= 0.0.12)
       trollop (~> 2.0)
 
@@ -15,10 +15,15 @@ GEM
       ZenTest (~> 4.3)
     ZenTest (4.9.5)
     ansi (1.4.3)
-    bettersam (0.0.1.alpha)
+    bettersam (0.0.2)
+      coveralls
+      rake
+      shoulda-context
+      simplecov
+      turn
     bio (1.4.3.0001)
-    biopsy (0.1.8)
-      rake (~> 10.3)
+    biopsy (0.1.9)
+      rake (~> 10.1)
       rubystats
       statsample
       threach
diff --git a/assemblotron.gemspec b/assemblotron.gemspec
index 0dabe94..2b057ea 100644
--- a/assemblotron.gemspec
+++ b/assemblotron.gemspec
@@ -13,8 +13,8 @@ Gem::Specification.new do |gem|
   gem.files = Dir['Rakefile', '{lib,test}/**/*', 'README*', 'LICENSE*']
   gem.require_paths = %w[ lib ]
 
-  gem.add_dependency 'rake', '~> 10.1'
-  gem.add_dependency 'biopsy', '0.1.8'
+  gem.add_dependency 'rake', '~> 10.3'
+  gem.add_dependency 'biopsy', '0.1.9'
   gem.add_dependency 'trollop', '~> 2.0'
   gem.add_dependency 'transrate', '0.0.12'
   gem.add_dependency 'RubyInline', '~> 3.12'
diff --git a/bin/atron b/bin/atron
index b0c8f93..fecf2d4 100755
--- a/bin/atron
+++ b/bin/atron
@@ -61,17 +61,17 @@ if cmd.nil?
 elsif cmd == "list"
   puts controller.list_assemblers
   exit
-elsif cmd == "run"
-  assembler = ARGV.shift
+# elsif cmd == "run"
+#   assembler = ARGV.shift
 elsif controller.assemblers.include?(cmd)
   assembler = cmd
   assembler_parser = controller.parser_for_assembler cmd
-  assembler_opts = Trollop::with_standard_exception_handling parser do
+  assembler_opts = Trollop::with_standard_exception_handling assembler_parser do
     raise Trollop::HelpNeeded if ARGV.empty? # show help screen
-    parser.parse ARGV
+    assembler_parser.parse ARGV
   end
 else
-  Trollop::die "unknown subcommand #{cmd.inspect}"
+  abort "unknown subcommand #{cmd.inspect}"
 end
 
 # run command
diff --git a/lib/assemblotron.rb b/lib/assemblotron.rb
index bd8d3f8..1bbb096 100644
--- a/lib/assemblotron.rb
+++ b/lib/assemblotron.rb
@@ -246,6 +246,8 @@ def run assembler
       if @global_opts[:optimiser] == 'tabu'
         algorithm = Biopsy::TabuSearch.new(a.parameters)
       elsif @global_opts[:optimiser] == 'sweeper'
+        p a.parameters
+        exit
         algorithm = Biopsy::ParameterSweeper.new(a.parameters)
       else
         raise NotImplementedError, "please select either tabu or\                                                     
diff --git a/lib/assemblotron/assemblers/soap_denovo_trans.yml b/lib/assemblotron/assemblers/soap_denovo_trans.yml
index 6d6598e..407623b 100644
--- a/lib/assemblotron/assemblers/soap_denovo_trans.yml
+++ b/lib/assemblotron/assemblers/soap_denovo_trans.yml
@@ -3,11 +3,6 @@ name: SoapDenovoTrans
 shortname: sdt
 output: {}
 parameters:
-  config:
-    type: string
-    opt: false
-    desc: 'Path to SoapDenovoTrans config file'
-    required: true
   left:
     type: string
     opt: false

From 0bdcc42c65c69bab6e84d206443aa062eb242436 Mon Sep 17 00:00:00 2001
From: Chris Boursnell <cboursnell@gmail.com>
Date: Fri, 25 Apr 2014 16:19:41 +0100
Subject: [PATCH 07/14] removed colons from config filename

---
 lib/assemblotron.rb                              | 1 -
 lib/assemblotron/assemblers/soap_denovo_trans.rb | 2 +-
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/lib/assemblotron.rb b/lib/assemblotron.rb
index 8fdd512..4740c15 100644
--- a/lib/assemblotron.rb
+++ b/lib/assemblotron.rb
@@ -248,7 +248,6 @@ def run assembler
         algorithm = Biopsy::TabuSearch.new(a.parameters)
       elsif @global_opts[:optimiser] == 'sweeper'
         p a.parameters
-        exit
         algorithm = Biopsy::ParameterSweeper.new(a.parameters)
       else
         raise NotImplementedError, "please select either tabu or\                                                     
diff --git a/lib/assemblotron/assemblers/soap_denovo_trans.rb b/lib/assemblotron/assemblers/soap_denovo_trans.rb
index 70ec548..7403169 100644
--- a/lib/assemblotron/assemblers/soap_denovo_trans.rb
+++ b/lib/assemblotron/assemblers/soap_denovo_trans.rb
@@ -98,7 +98,7 @@ def setup_full(global_opts, assembler_opts)
   # @return [String] full path to the generated config gile
   def create_config left, right, assembler_opts
     # create the config file
-    filename = "#{Time.now}.full.config".tr(" ","_")
+    filename = "#{Time.now}.full.config".tr(" ","_").tr(":",".")
     File.open(filename, 'w') do |f|
       f.puts 'max_rd_len=5000'
       f.puts '[LIB]'

From aa7875d89459b2d4ae5f2b7c0b1ef5fd6403aba6 Mon Sep 17 00:00:00 2001
From: Chris Boursnell <cboursnell@gmail.com>
Date: Tue, 29 Apr 2014 17:00:07 +0100
Subject: [PATCH 08/14] gemfile.lock changed again

---
 Gemfile.lock | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index e792742..b47f66b 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -3,9 +3,9 @@ PATH
   specs:
     assemblotron (0.0.2)
       RubyInline (~> 3.12)
-      biopsy (= 0.1.9)
+      biopsy (= 0.2.0)
       rake (~> 10.3)
-      transrate (= 0.0.12)
+      transrate (= 0.0.14)
       trollop (~> 2.0)
 
 GEM

From 6d14d2348584e192691e838442cfac9547b186c6 Mon Sep 17 00:00:00 2001
From: Chris Boursnell <cboursnell@gmail.com>
Date: Tue, 29 Apr 2014 17:05:29 +0100
Subject: [PATCH 09/14] actually doing stuff with the optimiser global option

---
 lib/assemblotron.rb | 16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

diff --git a/lib/assemblotron.rb b/lib/assemblotron.rb
index c326783..6f06e93 100644
--- a/lib/assemblotron.rb
+++ b/lib/assemblotron.rb
@@ -256,10 +256,24 @@ def run assembler
 
         # run the optimisation
         a.setup_optim(@global_opts, @assembler_opts)
+        start = nil
+        algorithm = nil
+        if @global_opts[:optimiser] == 'tabu'
+          algorithm = Biopsy::TabuSearch.new(a.parameters)
+        elsif @global_opts[:optimiser] == 'sweeper'
+          algorithm = Biopsy::ParameterSweeper.new(a.parameters)
+        elsif @global_opts[:optimiser].nil?
+          # this is fine
+        else
+          raise NotImplementedError, "please select either tabu or "+
+                                     "sweeper as the optimiser"
+        end
         e = Biopsy::Experiment.new(a, 
                                    options: @assembler_opts,
                                    threads: @global_opts[:threads],
-                                   verbosity: :loud)
+                                   start: start,
+                                   algorithm: algorithm,
+                                   verbosity: @global_opts[:verbosity].to_sym)
         res = e.run
 
         # write out the result

From 944d9ede51483a90864f38a9d44243e506790edc Mon Sep 17 00:00:00 2001
From: Chris Boursnell <cboursnell@gmail.com>
Date: Wed, 30 Apr 2014 12:01:22 +0100
Subject: [PATCH 10/14] fixed file path bug

---
 lib/assemblotron/assemblers/soap_denovo_trans.rb | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/lib/assemblotron/assemblers/soap_denovo_trans.rb b/lib/assemblotron/assemblers/soap_denovo_trans.rb
index 7403169..ea9c648 100644
--- a/lib/assemblotron/assemblers/soap_denovo_trans.rb
+++ b/lib/assemblotron/assemblers/soap_denovo_trans.rb
@@ -55,8 +55,8 @@ def run params
   def setup_optim(global_opts, assembler_opts)
     # setup config file for subsetted reads
     puts 'peforming setup for SoapDenovotrans optimisation'
-    left = assembler_opts[:left_subset]
-    right = assembler_opts[:right_subset]
+    left = File.expand_path(assembler_opts[:left_subset])
+    right = File.expand_path(assembler_opts[:right_subset])
     f = create_config(left, right, assembler_opts)
     assembler_opts[:config] = f
   end
@@ -80,8 +80,8 @@ def setup_optim(global_opts, assembler_opts)
   # @return undefined
   def setup_full(global_opts, assembler_opts)
     # set config file for full read set
-    left = assembler_opts[:left]
-    right = assembler_opts[:right]
+    left = File.expand_path(assembler_opts[:left])
+    right = File.expand_path(assembler_opts[:right])
     f = create_config(left, right, assembler_opts)
     assembler_opts[:config] = f
   end
@@ -167,7 +167,7 @@ def construct_command params
     cmd += " -e #{params[:e]}" # delete contigs with coverage no greater than
     cmd += " -t #{params[:t]}" # maximum number of transcripts from one locus
     cmd += " -G #{params[:G]}" # allowed length difference between estimated and filled gap
-    puts cmd
+    # puts cmd
     cmd
   end
 

From f38aaab30ada9c07ff3f678f6c44930246f52b37 Mon Sep 17 00:00:00 2001
From: Chris Boursnell <cboursnell@gmail.com>
Date: Thu, 29 May 2014 16:08:30 +0100
Subject: [PATCH 11/14] ignore config files

---
 .gitignore                            | 1 +
 2014-04-25_14:31:11_+0100.full.config | 1 -
 2 files changed, 1 insertion(+), 1 deletion(-)
 delete mode 100644 2014-04-25_14:31:11_+0100.full.config

diff --git a/.gitignore b/.gitignore
index ebb2906..ca53aae 100644
--- a/.gitignore
+++ b/.gitignore
@@ -13,6 +13,7 @@ test/version_tmp
 tmp
 *~
 *fastq
+*config
 
 # YARD artifacts
 .yardoc
diff --git a/2014-04-25_14:31:11_+0100.full.config b/2014-04-25_14:31:11_+0100.full.config
deleted file mode 100644
index 71df0b0..0000000
--- a/2014-04-25_14:31:11_+0100.full.config
+++ /dev/null
@@ -1 +0,0 @@
-max_rd_len=5000[LIB]avg_ins=reverse_seq=0asm_flags=3q1=/home/chris/documents/subset.Cd.keep.1q2=/home/chris/documents/subset.Cd.keep.2
\ No newline at end of file

From 602121e9dcbcbb022028f88d85a81835051814ba Mon Sep 17 00:00:00 2001
From: Chris Boursnell <cboursnell@gmail.com>
Date: Thu, 29 May 2014 16:10:45 +0100
Subject: [PATCH 12/14] added option to only do assembly and no scoring

---
 bin/atron           |  4 +++-
 lib/assemblotron.rb | 15 ++++++++++-----
 2 files changed, 13 insertions(+), 6 deletions(-)

diff --git a/bin/atron b/bin/atron
index feb6e3c..ceb70aa 100755
--- a/bin/atron
+++ b/bin/atron
@@ -50,9 +50,11 @@ EOS
   opt :subsample_size, "number of reads to use for optimisation",
       :default => 100_000
   opt :optimiser,
-      "Which optimiser to use. Possible: 'tabu' or 'sweeper' (default:'tabu')",
+      "Which optimiser to use. Possible: 'tabu' or 'sweeper'",
       :type => String, 
       :default => "tabu"
+  opt :only_assemble,
+      "If using parameter sweeper don't do any scoring, just run the assembler"
   opt :logfile, "write logs to file", :type => String
   opt :output_parameters,
       "file to which optimal parameters will be written",
diff --git a/lib/assemblotron.rb b/lib/assemblotron.rb
index 6f06e93..92d07c0 100644
--- a/lib/assemblotron.rb
+++ b/lib/assemblotron.rb
@@ -228,11 +228,13 @@ def final_assembly assembler, result
     def run assembler
       res = nil
       # load reference and create ublast DB
-      @assembler_opts[:reference] = 
-        Transrate::Assembly.new(@assembler_opts[:reference])
-      ra = Transrate::ReciprocalAnnotation.new(@assembler_opts[:reference],
-                                               @assembler_opts[:reference])
-      ra.make_reference_db
+      if !@global_opts[:only_assemble]
+        @assembler_opts[:reference] = 
+          Transrate::Assembly.new(@assembler_opts[:reference])
+        ra = Transrate::ReciprocalAnnotation.new(@assembler_opts[:reference],
+                                                 @assembler_opts[:reference])
+        ra.make_reference_db
+      end
 
       # setup the assembler
       a = self.get_assembler assembler
@@ -258,10 +260,13 @@ def run assembler
         a.setup_optim(@global_opts, @assembler_opts)
         start = nil
         algorithm = nil
+        
+        @settings.objectives_subset = ['assembly_score']
         if @global_opts[:optimiser] == 'tabu'
           algorithm = Biopsy::TabuSearch.new(a.parameters)
         elsif @global_opts[:optimiser] == 'sweeper'
           algorithm = Biopsy::ParameterSweeper.new(a.parameters)
+          @settings.objectives_subset = ['no_score'] if @global_opts[:only_assemble]
         elsif @global_opts[:optimiser].nil?
           # this is fine
         else

From 082f7ce123c0ba991feb8ea3e937b21b832d9e37 Mon Sep 17 00:00:00 2001
From: Chris Boursnell <cboursnell@gmail.com>
Date: Thu, 29 May 2014 16:11:36 +0100
Subject: [PATCH 13/14] the biopsy settings object now gets passed global
 options from atron

---
 lib/assemblotron.rb | 18 ++++++++++++------
 1 file changed, 12 insertions(+), 6 deletions(-)

diff --git a/lib/assemblotron.rb b/lib/assemblotron.rb
index 92d07c0..96c1692 100644
--- a/lib/assemblotron.rb
+++ b/lib/assemblotron.rb
@@ -25,7 +25,7 @@ module Assemblotron
   #   @return [Hash] the assembler-specific options
   class Controller
   
-    attr_accessor :global_opts
+    attr_reader :global_opts
     attr_accessor :assembler_opts
 
     # Creates a new Controller
@@ -53,14 +53,20 @@ def self.header
     # setting target and objectiv directories to those
     # provided with Assemblotron
     def init_settings
-      s = Biopsy::Settings.instance
-      s.set_defaults
+      @settings = Biopsy::Settings.instance
+      @settings.set_defaults
       libdir = File.dirname(__FILE__)
-      s.target_dir = [File.join(libdir, 'assemblotron/assemblers/')]
-      s.objectives_dir = [File.join(libdir, 'assemblotron/objectives/')]
+      @settings.target_dir = [File.join(libdir, 'assemblotron/assemblers/')]
+      @settings.objectives_dir = [File.join(libdir, 'assemblotron/objectives/')]
       @log.debug "initialised Biopsy settings"
     end # init_settings
 
+    def global_opts=(options)
+      @global_opts = options
+      @settings.keep_intermediates = true if @global_opts[:keep_intermediates]
+      @settings.gzip_intermediates = true if @global_opts[:gzip_intermediates]
+    end
+
     # Load global configuration from the config file at
     # +~/.assemblotron+, if it exists.
     def load_config
@@ -87,7 +93,7 @@ def load_config
     # one +.yml+ definition and one +.rb+ constructor per
     # assembler (see AssemblerDefinition).
     def load_assemblers
-      Biopsy::Settings.instance.target_dir.each do |dir|
+      @settings.target_dir.each do |dir|
         Dir.chdir dir do
           Dir['*.yml'].each do |file|
             name = File.basename(file, '.yml')

From 9749562ed9825bc074206ccda429a31ce10a0ae7 Mon Sep 17 00:00:00 2001
From: Chris Boursnell <cboursnell@gmail.com>
Date: Thu, 29 May 2014 16:12:50 +0100
Subject: [PATCH 14/14] objective that doesn't do anything and returns a score
 of 0

---
 lib/assemblotron/objectives/no_score.rb | 12 ++++++++++++
 1 file changed, 12 insertions(+)
 create mode 100644 lib/assemblotron/objectives/no_score.rb

diff --git a/lib/assemblotron/objectives/no_score.rb b/lib/assemblotron/objectives/no_score.rb
new file mode 100644
index 0000000..e6db862
--- /dev/null
+++ b/lib/assemblotron/objectives/no_score.rb
@@ -0,0 +1,12 @@
+# An objective function that returns 0
+#
+# This class conforms to the API for a Biopsy::ObjectiveFunction.
+class NoScore < Biopsy::ObjectiveFunction
+
+  # Don't do anything just return 0.
+  #
+  # @return [Integer] 0,
+  def run (raw_output, output_files, threads)
+    return 0
+  end
+end