if input.downcase.end_with?( "_ni.fasta" )
hmm_name = input[ 0 .. input.length - 10 ]
elsif input.downcase.end_with?( ".fasta" )
- id_norm = true
hmm_name = input[ 0 .. input.length - 7 ]
- puts
- puts "a. identifier normalization:"
- cmd = "#{TAP} #{input} #{hmm_name}_ni.fasta #{hmm_name}.nim"
- run_command( cmd )
- input = hmm_name + "_ni.fasta"
+ 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
- Dir.mkdir( hmm_name )
+ unless File.exist? hmm_name
+ Dir.mkdir( hmm_name )
+ end
puts
- puts "b. hmmscan:"
- 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 )
+ 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 "c. hmmscan to simple 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 )
+
+ 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 "d. domain table to forester format:"
- 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 )
+ 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 "e. dsx:"
- 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 )
+
+ dsx_output = "#{hmm_name}/#{hmm_name}__#{hmm_name}__ee#{e_value_exp.to_s}_#{length}"
+ unless File.exist? d2f_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.cp orig_input, "#{hmm_name}/#{orig_input}"
end
- Dir.mkdir( hmm_name + "/msa" )
- Dir.mkdir( hmm_name + "/msa100" )
+ 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
- FileUtils.cp "#{hmm_name}/#{hmm_name}__#{hmm_name}__ee#{e_value_exp.to_s}_#{length}.fasta", "#{hmm_name}/msa/#{hmm_name}__#{hmm_name}__ee#{e_value_exp.to_s}_#{length}"
- FileUtils.cp "#{hmm_name}/#{hmm_name}__#{hmm_name}__ee#{e_value_exp.to_s}_#{length}.fasta", "#{hmm_name}/msa100/#{hmm_name}__#{hmm_name}__ee#{e_value_exp.to_s}_#{length}"
+ FileUtils.cp "#{dsx_output}.fasta", "#{msa_dir}/#{dsx_output}"
+ FileUtils.cp "#{dsx_output}.fasta", "#{msa_100_dir}/#{dsx_output}"
- if File.exists?( TEMPLATE_FILE )
- FileUtils.cp TEMPLATE_FILE, "#{hmm_name}/msa/"
- FileUtils.cp TEMPLATE_FILE, "#{hmm_name}/msa100/"
+ if File.exist?( TEMPLATE_FILE )
+ FileUtils.cp TEMPLATE_FILE, msa_dir
+ FileUtils.cp TEMPLATE_FILE, msa_100_dir
if LAUNCH_ANALYSIS
puts "f. analysis:"
- Dir.chdir "#{hmm_name}/msa/"
+ Dir.chdir msa_dir
run_command "#{PF} -b=1 -s"
Dir.chdir "../.."
- Dir.chdir "#{hmm_name}/msa100/"
+ Dir.chdir msa_100_dir
run_command "#{PF} -b=100 -s"
Dir.chdir "../.."
puts