- if do_domain_combination_analysis
-
- puts "hmmscan:"
- cmd = "#{hmmscan} --nobias --domtblout #{base_name}_hmmscan_10 -E 10 #{PFAM}Pfam-A.hmm #{input}"
- run_command( cmd )
- puts
-
- puts "hmmscan to simple domain table:"
- cmd = "#{hsp} #{base_name}_hmmscan_10 #{base_name}_hmmscan_10_domain_table"
- run_command( cmd )
- puts
-
- puts "domain table to forester format:"
- cmd = "#{d2f} -e=10 #{base_name}_hmmscan_10_domain_table #{input} #{base_name}_hmmscan_10.dff"
- run_command( cmd )
- puts