From 68fc457b73ae13f44a559db01b17203a18cc77ad Mon Sep 17 00:00:00 2001
From: "cmzmasek@gmail.com"
 <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Wed, 3 Jul 2013 22:32:15 +0000
Subject: [PATCH] inprogress

---
 forester/ruby/scripts/copy.rb |   10 ++++++++++
 forester/ruby/scripts/g.rb    |    2 +-
 forester/ruby/scripts/gl.rb   |    9 +++++++++
 3 files changed, 20 insertions(+), 1 deletion(-)
 create mode 100644 forester/ruby/scripts/copy.rb
 create mode 100644 forester/ruby/scripts/gl.rb

diff --git a/forester/ruby/scripts/copy.rb b/forester/ruby/scripts/copy.rb
new file mode 100644
index 0000000..2263329
--- /dev/null
+++ b/forester/ruby/scripts/copy.rb
@@ -0,0 +1,10 @@
+require 'fileutils'
+Dir.foreach(".") do |f|
+  next if f == '.' or f == '..'
+  if f =~ /^([A-Z0-9]{3,5}).*\..+/
+    tax = $1
+    FileUtils.cp f, "all/" + tax + ".fasta"
+  elsif 
+    puts "ignored " + f.to_s
+  end
+end
\ No newline at end of file
diff --git a/forester/ruby/scripts/g.rb b/forester/ruby/scripts/g.rb
index 6d1adf4..a4ccd52 100644
--- a/forester/ruby/scripts/g.rb
+++ b/forester/ruby/scripts/g.rb
@@ -1,6 +1,6 @@
 File.open( "g" ) do | file |
   while line = file.gets
-    if line =~ /^(\S{3,5})\s+\S{3,5}/
+    if line =~ /^([A-Z0-9]{3,5})/
       puts "/home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/" + $1 + ".hmmscan    " + $1
     else
       puts line
diff --git a/forester/ruby/scripts/gl.rb b/forester/ruby/scripts/gl.rb
new file mode 100644
index 0000000..ebb99a9
--- /dev/null
+++ b/forester/ruby/scripts/gl.rb
@@ -0,0 +1,9 @@
+File.open( "gl.txt" ) do | file |
+  while line = file.gets
+    if line =~ /^([A-Z0-9]{3,5})/
+      puts $1 + "\t" + "/home/czmasek/DATA/SEQUENCES/GENOMES/PROTEIN_PREDICTIONS_CDHIT_095/ALL/" + $1 + ".fasta"
+    else
+      puts line
+    end
+  end
+end
\ No newline at end of file
-- 
1.7.10.2