#!/usr/local/bin/ruby -w
+if ( ARGV == nil || ARGV.length != 2 )
+ puts( "usage: preprocess.rb <input> <path to Pfam A HMMs>" )
+ exit( -1 )
+end
+
input = ARGV[ 0 ]
-system( "hmmscan --nobias --domtblout " + input + "_hmmscan_260_10 -E 10 Pfam-A.hmm " + input + ".ni.fasta" )
+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" )