From d95f7fa8d5be9cf5a74a4e82c9493afcf9013a61 Mon Sep 17 00:00:00 2001
From: "cmzmasek@gmail.com"
 <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Fri, 19 Oct 2012 05:59:55 +0000
Subject: [PATCH] in progress

---
 .../evoruby/lib/evo/io/parser/hmmscan_parser.rb    |   85 ++++++++++++++++++++
 1 file changed, 85 insertions(+)
 create mode 100644 forester/ruby/evoruby/lib/evo/io/parser/hmmscan_parser.rb

diff --git a/forester/ruby/evoruby/lib/evo/io/parser/hmmscan_parser.rb b/forester/ruby/evoruby/lib/evo/io/parser/hmmscan_parser.rb
new file mode 100644
index 0000000..c148cdf
--- /dev/null
+++ b/forester/ruby/evoruby/lib/evo/io/parser/hmmscan_parser.rb
@@ -0,0 +1,85 @@
+#
+# To change this template, choose Tools | Templates
+# and open the template in the editor.
+
+
+class HmmscanParser
+
+  def initialize file
+    @file = file
+  end
+
+  def parse
+    results = []
+    File.open( @file ).each do | line |
+      line.strip!
+      if !line.empty? && line[ 0 ] != "#"
+        results << parse_line( line )
+      end
+    end
+    results
+  end
+
+  def parse_line( line )
+    #         tn      acc     tlen    query   acc     qlen    Evalue  score   bias    #       of      c-E     i-E     score   bias    hf      ht      af      at      ef      et      acc     desc
+    #         1       2       3       4       5       6       7       8       9       10      11      12      13      14      15      16      17      18      19      20      21      22      23
+    if line =~ /^(\S+)\s+(\S+)\s+(\d+)\s+(\S+)\s+(\S+)\s+(\d+)\s+(\S+)\s+(\S+)\s+(\S+)\s+(\d+)\s+(\d+)\s+(\S+)\s+(\S+)\s+(\S+)\s+(\S+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\S+)\s+(.*)/
+
+      r = HmmscanResult.new
+
+      r.model      = $1
+      r.tlen       = $3.to_i
+      r.query      = $4
+      r.qlen       = $6.to_i
+
+      r.fs_e_value = $7.to_f
+      r.fs_score   = $8.to_f
+
+      r.number     = $10.to_i
+      r.out_of     = $11.to_i
+
+      r.c_e_value  = $12.to_f
+      r.i_e_value  = $13.to_f
+      r.score      = $14.to_f
+
+      r.hmm_from   = $16.to_i
+      r.hmm_to     = $17.to_i
+
+      r.ali_from   = $18.to_i
+      r.ali_to     = $19.to_i
+
+      r.env_from   = $20.to_i
+      r.env_to     = $21.to_i
+
+      if r.number > r.out_of || r.hmm_from > r.hmm_to || r.ali_from > r.ali_to || r.env_from > r.env_to
+        raise IOError, "illogical format: " + line
+      end
+
+      r
+    else
+      raise IOError, "illegal format: " + line
+    end
+  end
+end
+
+class HmmscanResult
+
+  attr_accessor :model
+  attr_accessor :tlen
+  attr_accessor :query
+  attr_accessor :qlen
+  attr_accessor :fs_e_value
+  attr_accessor :fs_score
+  attr_accessor :number
+  attr_accessor :out_of
+  attr_accessor :c_e_value
+  attr_accessor :i_e_value
+  attr_accessor :score
+  attr_accessor :hmm_from
+  attr_accessor :hmm_to
+  attr_accessor :ali_from
+  attr_accessor :ali_to
+  attr_accessor :env_from
+  attr_accessor :env_to
+
+end
-- 
1.7.10.2