v 1.04

[jalview.git] / forester / ruby / evoruby / exe / run_phylo_pipeline_x.rb

diff --git a/forester/ruby/evoruby/exe/run_phylo_pipeline_x.rb b/forester/ruby/evoruby/exe/run_phylo_pipeline_x.rb
index 0727eb7..1711880 100644 (file)
--- a/forester/ruby/evoruby/exe/run_phylo_pipeline_x.rb
+++ b/forester/ruby/evoruby/exe/run_phylo_pipeline_x.rb
@@ -15,7 +15,7 @@ module Evoruby
 
   class RunPhyloPipeline
 
-    LAUNCH_ANALYSIS = true
+    LAUNCH_ANALYSIS = false
     HOME          = "/home/czmasek/"
     FORESTER_RUBY = "#{HOME}SOFTWARE/FORESTER/DEV/forester/forester/ruby/evoruby/exe/"
     PFAM          = "#{HOME}DATA/PFAM/PFAM270X/"
@@ -58,6 +58,8 @@ module Evoruby
 
       input_files = Dir.entries(".").select { |f| !File.directory?( f ) && f.downcase.end_with?( ".fasta" ) }
 
+      input_files.sort!
+
       puts "Input files:"
       input_files.each do | input |
         puts input
@@ -91,7 +93,7 @@ module Evoruby
             unless File.exist? input
               error "expected to already exist: " + input
             end
-            puts "a. identifier normalization already done:" + input
+            puts "a. identifier normalization already done: " + input
           end
         else
           error "illegal name: " + input
@@ -133,14 +135,14 @@ module Evoruby
         end
         puts
 
-
-        dsx_output = "#{hmm_name}/#{hmm_name}__#{hmm_name}__ee#{e_value_exp.to_s}_#{length}"
-        unless File.exist? d2f_output
+        dsx_output_base = "#{hmm_name}__#{hmm_name}__ee#{e_value_exp.to_s}_#{length}"
+        dsx_output = hmm_name +"/" + dsx_output_base
+        unless File.exist? dsx_output + ".fasta"
           puts "e. dsx:"
           cmd = "#{DSX} -d -e=1e-#{e_value_exp.to_s} -l=#{length} #{hmm_name} #{hmmscan_output} #{input} #{dsx_output}"
           run_command( cmd )
         else
-          puts "e. dsx output already exists: " + dsx_output
+          puts "e. dsx output already exists: " + dsx_output + ".fasta"
         end
         puts
 
@@ -160,21 +162,39 @@ module Evoruby
           Dir.mkdir( msa_100_dir )
         end
 
-        FileUtils.cp "#{dsx_output}.fasta", "#{msa_dir}/#{dsx_output}"
-        FileUtils.cp "#{dsx_output}.fasta", "#{msa_100_dir}/#{dsx_output}"
+        run_1 = false
+        run_100 = false
+
+        unless File.exist? "#{msa_dir}/#{dsx_output_base}"
+          run_1 = true
+          FileUtils.cp "#{dsx_output}.fasta", "#{msa_dir}/#{dsx_output_base}"
+        end
+
+        unless File.exist? "#{msa_100_dir}/#{dsx_output_base}"
+          run_100 = true
+          FileUtils.cp "#{dsx_output}.fasta", "#{msa_100_dir}/#{dsx_output_base}"
+        end
 
         if File.exist?( TEMPLATE_FILE )
-          FileUtils.cp TEMPLATE_FILE, msa_dir
-          FileUtils.cp TEMPLATE_FILE, msa_100_dir
+          if run_1
+            FileUtils.cp TEMPLATE_FILE, msa_dir
+          end
+          if run_100
+            FileUtils.cp TEMPLATE_FILE, msa_100_dir
+          end
 
-          if LAUNCH_ANALYSIS
+          if LAUNCH_ANALYSIS && ( run_1 || run_100 )
             puts "f. analysis:"
-            Dir.chdir msa_dir
-            run_command "#{PF} -b=1 -s"
-            Dir.chdir "../.."
-            Dir.chdir msa_100_dir
-            run_command "#{PF} -b=100 -s"
-            Dir.chdir "../.."
+            if run_1
+              Dir.chdir msa_dir
+              run_command "#{PF} -b=1 -s"
+              Dir.chdir "../.."
+            end
+            if run_100
+              Dir.chdir msa_100_dir
+              run_command "#{PF} -b=100 -s"
+              Dir.chdir "../.."
+            end
             puts
           end
         end