From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Thu, 13 Sep 2012 00:02:00 +0000 (+0000)
Subject: in progress
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=772ac6aa39af98574111799085fa39dd0b3f6e73;p=jalview.git

in progress
---

diff --git a/forester/ruby/evoruby/exe/fasta_compare.rb b/forester/ruby/evoruby/exe/fasta_compare.rb
new file mode 100755
index 0000000..45c8cb1
--- /dev/null
+++ b/forester/ruby/evoruby/exe/fasta_compare.rb
@@ -0,0 +1,58 @@
+#!/usr/local/bin/ruby -w
+
+require 'lib/evo/sequence/sequence'
+require 'lib/evo/msa/msa'
+require 'lib/evo/msa/msa_factory'
+require 'lib/evo/io/writer/fasta_writer'
+require 'lib/evo/io/parser/fasta_parser'
+
+module Evoruby
+
+  input1 = ARGV[ 0 ]
+  input2 = ARGV[ 1 ]
+
+  f = MsaFactory.new()
+
+  msa1 = nil
+  msa2 = nil
+
+  begin
+    msa1 = f.create_msa_from_file( input1, FastaParser.new() )
+    msa2 = f.create_msa_from_file( input2, FastaParser.new() )
+  rescue Exception => e
+    puts "error: " + e.to_s
+    exit
+  end
+
+  only_in_1 = Msa.new
+  only_in_2 = Msa.new
+  in_both = Msa.new
+
+  for i in 0 ... msa1.get_number_of_seqs()
+    seq = msa1.get_sequence( i )
+    name = seq.get_name
+    if msa2.has?( name )
+      in_both.add_sequence(seq)
+    else
+      only_in_1.add_sequence(seq)
+    end
+  end
+
+  for j in 0 ... msa2.get_number_of_seqs()
+    seq = msa2.get_sequence( j )
+    name = seq.get_name
+    unless msa1.has?( name )
+      only_in_2.add_sequence(seq)
+    end
+  end
+
+  puts "only in 1: " + only_in_1.get_number_of_seqs.to_s
+  puts "only in 2: " + only_in_2.get_number_of_seqs.to_s
+  puts "in both  : " + in_both.get_number_of_seqs.to_s
+
+  w = FastaWriter.new
+  w.write(only_in_1, "only_in_1.fasta")
+  w.write(only_in_2, "only_in_2.fasta")
+  w.write(in_both, "in_both.fasta")
+
+end