error "arguments are: <min-length> " +
"<neg E-value exponent for domain extraction> [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
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" )
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