forester/ruby/scripts/preprocess.rb

   1 #!/usr/local/bin/ruby -w
   2
   3
   4 if ( ARGV == nil || ARGV.length != 3 )
   5   puts( "usage: preprocess.rb <input> <path to Pfam A HMMs>" )
   6   exit( -1 )
   7 end
   8
   9 input = ARGV[ 0 ]
  10
  11 pfam = ARGV[ 1 ]
  12
  13 system( "hmmscan --nobias --domtblout " + input + "_hmmscan_260_10 -E 10 " + pfam + " "  + input + ".ni.fasta" )
  14
  15 system( "hsp " + input + "_hmmscan_260_10 " + input + "_hmmscan_260_10_domain_table" )
  16
  17 system( "d2f " + input + "_hmmscan_260_10_domain_table " + input + ".ni.fasta " + input + "_hmmscan_260_10.dff" )