From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Wed, 21 Mar 2012 04:21:25 +0000 (+0000)
Subject: in progress
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=75f9103b756a1ebd10cc1f6a6d987ce4fb6c6a88;p=jalview.git

in progress
---

diff --git a/forester/ruby/scripts/preprocess.rb b/forester/ruby/scripts/preprocess.rb
new file mode 100644
index 0000000..f3447ef
--- /dev/null
+++ b/forester/ruby/scripts/preprocess.rb
@@ -0,0 +1,10 @@
+#!/usr/local/bin/ruby -w
+
+
+input = ARGV[ 0 ]
+
+system( "hmmscan --nobias --domtblout " + input + "_hmmscan_260_10 -E 10 Pfam-A.hmm " + 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" )
\ No newline at end of file