X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fruby%2Fevoruby%2Fexe%2Frun_phylo_pipeline_x.rb;h=e07a6205d92de414c9fbca6d5b96b9ff682780c8;hb=56e0222aa798aed2a460ecda79d5c48104668c9c;hp=cc8cfbb948b0442c853b1f41892003a28927c1ca;hpb=80ae355701e22009bbbeccfb2a0b4456f7fa1164;p=jalview.git diff --git a/forester/ruby/evoruby/exe/run_phylo_pipeline_x.rb b/forester/ruby/evoruby/exe/run_phylo_pipeline_x.rb index cc8cfbb..e07a620 100644 --- a/forester/ruby/evoruby/exe/run_phylo_pipeline_x.rb +++ b/forester/ruby/evoruby/exe/run_phylo_pipeline_x.rb @@ -9,26 +9,30 @@ # # +require 'fileutils' module Evoruby class RunPhyloPipeline - PFAM = "/home/czmasek/DATA/PFAM/PFAM270X/" - HMMSCAN = "/home/czmasek/SOFTWARE/HMMER/hmmer-3.0/src/hmmscan" - HSP = "/home/czmasek/SOFTWARE/FORESTER/DEV/forester/forester/ruby/evoruby/exe/hsp.rb" - D2F = "/home/czmasek/SOFTWARE/FORESTER/DEV/forester/forester/ruby/evoruby/exe/d2f.rb" - DSX = "/home/czmasek/SOFTWARE/FORESTER/DEV/forester/forester/ruby/evoruby/exe/dsx.rb" - TAP = "/home/czmasek/SOFTWARE/FORESTER/DEV/forester/forester/ruby/evoruby/exe/tap.rb" + LAUNCH_ANALYSIS = true + HOME = "/home/czmasek/" + FORESTER_RUBY = "#{HOME}SOFTWARE/FORESTER/DEV/forester/forester/ruby/evoruby/exe/" + PFAM = "#{HOME}DATA/PFAM/PFAM270X/" + HMMSCAN = "#{HOME}SOFTWARE/HMMER/hmmer-3.0/src/hmmscan" + HSP = "#{FORESTER_RUBY}hsp.rb" + D2F = "#{FORESTER_RUBY}d2f.rb" + DSX = "#{FORESTER_RUBY}dsx.rb" + TAP = "#{FORESTER_RUBY}tap.rb" + PF = "#{FORESTER_RUBY}phylogeny_factory.rb" + TEMPLATE_FILE = '00_phylogeny_factory.template' def run - unless ARGV.length >= 4 && ARGV.length <= 6 + unless ARGV.length >= 2 && ARGV.length <= 4 error "arguments are: " + " [E-value for hmmscan, default is 10] [hmmscan option, default is --nobias, --max for no heuristics]" end - - length = ARGV[ 0 ].to_i e_value_exp = ARGV[ 1 ].to_i @@ -60,44 +64,139 @@ module Evoruby end puts + counter = 1 input_files.each do | input | + puts counter.to_s + "/" + input_files.size.to_s + " " + input + ": " + + counter += 1 + hmm_name = "" + id_norm = false + orig_input = input if input.downcase.end_with?( "_ni.fasta" ) hmm_name = input[ 0 .. input.length - 10 ] elsif input.downcase.end_with?( ".fasta" ) hmm_name = input[ 0 .. input.length - 7 ] - puts - puts "0. identifier normalization:" - cmd = "#{TAP} #{input}" - run_command( cmd ) - puts + unless File.exist? hmm_name + id_norm = true + puts + puts "a. identifier normalization:" + cmd = "#{TAP} #{input} #{hmm_name}_ni.fasta #{hmm_name}.nim" + run_command( cmd ) + input = hmm_name + "_ni.fasta" + else + input = hmm_name + "/" + hmm_name + "_ni.fasta" + unless File.exist? input + error "expected to already exist: " + input + end + puts "a. identifier normalization already done:" + input + end else error "illegal name: " + input end + unless File.exist? hmm_name + Dir.mkdir( hmm_name ) + end + puts - puts "1. hmmscan:" - cmd = "#{HMMSCAN} #{hmmscan_option} --domtblout #{hmm_name}_hmmscan_#{e_for_hmmscan.to_s} -E #{e_for_hmmscan.to_s} #{PFAM}Pfam-A.hmm #{input}" - run_command( cmd ) + hmmscan_output = hmm_name + "/" + hmm_name + "_hmmscan_" + e_for_hmmscan.to_s + unless File.exist? hmmscan_output + puts "b. hmmscan:" + cmd = "#{HMMSCAN} #{hmmscan_option} --domtblout #{hmmscan_output} -E #{e_for_hmmscan.to_s} #{PFAM}Pfam-A.hmm #{input}" + run_command( cmd ) + else + puts "b. hmmscan output already exists: " + hmmscan_output + end puts - puts "2. hmmscan to simple domain table:" - cmd = "#{HSP} #{hmm_name}_hmmscan_#{e_for_hmmscan.to_s} #{hmm_name}_hmmscan_#{e_for_hmmscan.to_s}_domain_table" - run_command( cmd ) + + hsp_output = hmm_name + "/" + hmm_name + "_hmmscan_#{e_for_hmmscan.to_s}_domain_table" + unless File.exist? hsp_output + puts "c. hmmscan to simple domain table:" + cmd = "#{HSP} #{hmmscan_output} #{hsp_output}" + run_command( cmd ) + else + puts "c. hmmscan to simple domain table output already exists: " + hsp_output + end puts - puts "3. domain table to forester format:" - cmd = "#{D2F} -e=10 #{hmm_name}_hmmscan_#{e_for_hmmscan.to_s}_domain_table #{input} #{hmm_name}_hmmscan_#{e_for_hmmscan.to_s}.dff" - run_command( cmd ) + d2f_output = "#{hmm_name}/#{hmm_name}_hmmscan_#{e_for_hmmscan.to_s}.dff" + unless File.exist? d2f_output + puts "d. domain table to forester format:" + cmd = "#{D2F} -e=10 #{hsp_output} #{input} #{d2f_output}" + run_command( cmd ) + else + puts "d. domain table to forester format output already exists: " + d2f_output + end puts - puts "4. dsx:" - cmd = "#{DSX} -d -e=1e-#{e_value_exp.to_s} -l=#{length} #{hmm_name} #{hmm_name}_hmmscan_#{e_for_hmmscan.to_s} #{input} #{hmm_name}__#{hmm_name}__ee#{e_value_exp.to_s}_#{length}" - run_command( cmd ) + + dsx_output = "#{hmm_name}/#{hmm_name}__#{hmm_name}__ee#{e_value_exp.to_s}_#{length}" + unless File.exist? dsx_output + 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 + end puts + if id_norm + FileUtils.mv "#{hmm_name}_ni.fasta", "#{hmm_name}/#{hmm_name}_ni.fasta" + FileUtils.mv "#{hmm_name}.nim", "#{hmm_name}/#{hmm_name}.nim" + FileUtils.cp orig_input, "#{hmm_name}/#{orig_input}" + end + + msa_dir = hmm_name + "/msa_ee#{e_value_exp.to_s}_#{length}" + msa_100_dir =hmm_name + "/msa100_ee#{e_value_exp.to_s}_#{length}" + + unless File.exist? msa_dir + Dir.mkdir( msa_dir ) + end + unless File.exist? msa_100_dir + Dir.mkdir( msa_100_dir ) + end + + run_1 = false + run_100 = false + + unless File.exist? "#{msa_dir}/#{dsx_output}" + run_1 = true + FileUtils.cp "#{dsx_output}.fasta", "#{msa_dir}/#{dsx_output}" + end + + unless File.exist? "#{msa_100_dir}/#{dsx_output}" + run_100 = true + FileUtils.cp "#{dsx_output}.fasta", "#{msa_100_dir}/#{dsx_output}" + end + + if File.exist?( TEMPLATE_FILE ) + if run_1 + FileUtils.cp TEMPLATE_FILE, msa_dir + end + if run_100 + FileUtils.cp TEMPLATE_FILE, msa_100_dir + end + + if LAUNCH_ANALYSIS + puts "f. analysis:" + 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 + end end