#!/usr/local/bin/ruby -w
if ( ARGV == nil || ARGV.length != 2 )
puts( "usage: preprocess.rb " )
exit( -1 )
end
input = ARGV[ 0 ]
pfam = ARGV[ 1 ]
system( "hmmscan --nobias --domtblout " + input + "_hmmscan_260_10 -E 10 " + pfam + " " + input + ".ni.fasta" )
system( "hsp " + input + "_hmmscan_260_10 " + input + "_hmmscan_260_10_domain_table" )
system( "d2f " + input + "_hmmscan_260_10_domain_table " + input + ".ni.fasta " + input + "_hmmscan_260_10.dff" )