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domain + go output work begins
[jalview.git]
/
forester
/
ruby
/
scripts
/
preprocess.rb
diff --git
a/forester/ruby/scripts/preprocess.rb
b/forester/ruby/scripts/preprocess.rb
index
f3447ef
..
2cc1479
100644
(file)
--- a/
forester/ruby/scripts/preprocess.rb
+++ b/
forester/ruby/scripts/preprocess.rb
@@
-1,9
+1,16
@@
#!/usr/local/bin/ruby -w
#!/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 ]
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" )
system( "hsp " + input + "_hmmscan_260_10 " + input + "_hmmscan_260_10_domain_table" )