inprogress

diff --git a/forester/ruby/scripts/nffas_parse.rb b/forester/ruby/scripts/nffas_parse.rb
new file mode 100755 (executable)
index 0000000..645d44d
--- /dev/null
+++ b/forester/ruby/scripts/nffas_parse.rb
@@ -0,0 +1,13 @@
+#!/usr/local/bin/ruby -w
+
+infile = ARGV[ 0 ]
+
+File.open( infile ) do | file |
+  while line = file.gets
+    if line =~ /^>>(.+)/
+      puts ">" + $1
+    elsif line =~ /^([A-Z]+)/
+      puts $1
+    end
+  end
+end

diff --git a/forester/ruby/scripts/x.rb b/forester/ruby/scripts/x.rb
index cb70c70..883b215 100644 (file)
--- a/forester/ruby/scripts/x.rb
+++ b/forester/ruby/scripts/x.rb
@@ -6,10 +6,10 @@ Dir.foreach(".") do |f|
     cmd = "#{PRG} -ie=10 -a -pe=1 -m=RRMa -s=#{taxon} #{taxon}.hmmscan_260 #{taxon}_ie10_domain_table > #{taxon}_ie10_summary_table.txt"
     puts cmd
     output = IO.popen( cmd )
-  elsif f =~ /^([A-Z0-9]{3,6})_cdhit090\.hmmscan_260/  
+  elsif f =~ /^([A-Z0-9]{3,6})_cdhit090\.hmmscan_260/
     taxon = $1
     cmd = "#{PRG} -ie=10 -a -pe=1 -m=RRMa -s=#{taxon} #{taxon}_cdhit090.hmmscan_260 #{taxon}_cdhit090_ie10_domain_table > #{taxon}_cdhit090_ie10_summary_table.txt"
     puts cmd
     output = IO.popen( cmd )
-  end  
+  end
 end
\ No newline at end of file