X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fruby%2Fscripts%2Fpreprocess.rb;h=2cc1479f4bedc57141954439d5fca9ae728643dd;hb=5c4e24e304f57058fa1c3a3f1256a573b37d89f6;hp=f3447efbf407f57983d71f43f45ee8153811041a;hpb=75f9103b756a1ebd10cc1f6a6d987ce4fb6c6a88;p=jalview.git

diff --git a/forester/ruby/scripts/preprocess.rb b/forester/ruby/scripts/preprocess.rb
index f3447ef..2cc1479 100644
--- a/forester/ruby/scripts/preprocess.rb
+++ b/forester/ruby/scripts/preprocess.rb
@@ -1,9 +1,16 @@
 #!/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" )