From 7926b7cbff230f99b6cd4202c386a03429ae3262 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Sat, 9 Nov 2013 04:41:12 +0000 Subject: [PATCH] inprogress --- forester/ruby/evoruby/exe/run_phylo_pipeline_x.rb | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/forester/ruby/evoruby/exe/run_phylo_pipeline_x.rb b/forester/ruby/evoruby/exe/run_phylo_pipeline_x.rb index 05507b9..25224de 100644 --- a/forester/ruby/evoruby/exe/run_phylo_pipeline_x.rb +++ b/forester/ruby/evoruby/exe/run_phylo_pipeline_x.rb @@ -26,7 +26,7 @@ module Evoruby 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 @@ -62,9 +62,9 @@ module Evoruby input_files.each do | input | puts counter.to_s + "/" + input_files.size.to_s + " " + input + ": " - + counter += 1 - + hmm_name = "" if input.downcase.end_with?( "_ni.fasta" ) @@ -80,24 +80,26 @@ module Evoruby error "illegal name: " + input end + Dir.mkdir( hmm_name ) + puts puts "b. 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}" + cmd = "#{HMMSCAN} #{hmmscan_option} --domtblout #{hmm_name}/#{hmm_name}_hmmscan_#{e_for_hmmscan.to_s} -E #{e_for_hmmscan.to_s} #{PFAM}Pfam-A.hmm #{input}" run_command( cmd ) puts puts "c. 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" + cmd = "#{HSP} #{hmm_name}/#{hmm_name}_hmmscan_#{e_for_hmmscan.to_s} #{hmm_name}/#{hmm_name}_hmmscan_#{e_for_hmmscan.to_s}_domain_table" run_command( cmd ) puts puts "d. 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" + cmd = "#{D2F} -e=10 #{hmm_name}/#{hmm_name}_hmmscan_#{e_for_hmmscan.to_s}_domain_table #{input} #{hmm_name}/#{hmm_name}_hmmscan_#{e_for_hmmscan.to_s}.dff" run_command( cmd ) puts puts "e. 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}" + cmd = "#{DSX} -d -e=1e-#{e_value_exp.to_s} -l=#{length} #{hmm_name} #{hmm_name}/#{hmm_name}_hmmscan_#{e_for_hmmscan.to_s} #{input} #{hmm_name}/#{hmm_name}__#{hmm_name}__ee#{e_value_exp.to_s}_#{length}" run_command( cmd ) puts -- 1.7.10.2