From 790849e542e581631f0b757becfba72a5f6f1b58 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Wed, 21 Mar 2012 04:23:35 +0000 Subject: [PATCH 1/1] in progress --- forester/ruby/scripts/preprocess.rb | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/forester/ruby/scripts/preprocess.rb b/forester/ruby/scripts/preprocess.rb index f3447ef..8829eb6 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 != 3 ) + puts( "usage: preprocess.rb " ) + 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" ) -- 1.7.10.2