added bin_vals biopiece and tests

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1088 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/bin_vals b/bp_bin/bin_vals
new file mode 100755 (executable)
index 0000000..42fb7d6
--- /dev/null
+++ b/bp_bin/bin_vals
@@ -0,0 +1,54 @@
+#!/usr/bin/env ruby
+
+# Copyright (C) 2007-2010 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# This program is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Bins values to a specfied key from records in the stream.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+require 'biopieces'
+
+casts = []
+casts << {:long=>'key',      :short=>'k', :type=>'string', :mandatory=>true, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'bin_size', :short=>'b', :type=>'uint',   :mandatory=>true, :default=>10,  :allowed=>nil, :disallowed=>'0'}
+
+bp = Biopieces.new
+
+options = bp.parse(ARGV, casts)
+
+bp.each_record do |record|
+  if record.has_key? options[:key]
+    record[(options[:key].to_s + "_BIN").to_sym] = (record[options[:key]].to_i / options[:bin_size]) * options[:bin_size]
+  end
+
+  bp.puts record
+end
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__

diff --git a/bp_test/in/bin_vals.in b/bp_test/in/bin_vals.in
new file mode 100644 (file)
index 0000000..f5b7f18
--- /dev/null
+++ b/bp_test/in/bin_vals.in
@@ -0,0 +1,20 @@
+V0: 1
+---
+V0: 2
+---
+V0: 3
+---
+V0: 4
+---
+V0: 5
+---
+V0: 6
+---
+V0: 7
+---
+V0: 8
+---
+V0: 9
+---
+V0: 10
+---

diff --git a/bp_test/out/bin_vals.out.1 b/bp_test/out/bin_vals.out.1
new file mode 100644 (file)
index 0000000..c1845d7
--- /dev/null
+++ b/bp_test/out/bin_vals.out.1
@@ -0,0 +1,30 @@
+V0: 1
+V0_BIN: 0
+---
+V0: 2
+V0_BIN: 0
+---
+V0: 3
+V0_BIN: 0
+---
+V0: 4
+V0_BIN: 0
+---
+V0: 5
+V0_BIN: 0
+---
+V0: 6
+V0_BIN: 0
+---
+V0: 7
+V0_BIN: 0
+---
+V0: 8
+V0_BIN: 0
+---
+V0: 9
+V0_BIN: 0
+---
+V0: 10
+V0_BIN: 10
+---

diff --git a/bp_test/out/bin_vals.out.2 b/bp_test/out/bin_vals.out.2
new file mode 100644 (file)
index 0000000..f526ff1
--- /dev/null
+++ b/bp_test/out/bin_vals.out.2
@@ -0,0 +1,30 @@
+V0: 1
+V0_BIN: 0
+---
+V0: 2
+V0_BIN: 0
+---
+V0: 3
+V0_BIN: 0
+---
+V0: 4
+V0_BIN: 0
+---
+V0: 5
+V0_BIN: 5
+---
+V0: 6
+V0_BIN: 5
+---
+V0: 7
+V0_BIN: 5
+---
+V0: 8
+V0_BIN: 5
+---
+V0: 9
+V0_BIN: 5
+---
+V0: 10
+V0_BIN: 10
+---

diff --git a/bp_test/test/test_bin_vals b/bp_test/test/test_bin_vals
new file mode 100755 (executable)
index 0000000..e537d2b
--- /dev/null
+++ b/bp_test/test/test_bin_vals
@@ -0,0 +1,11 @@
+#!/bin/bash
+
+source "$BP_DIR/bp_test/lib/test.sh"
+
+run "$bp -I $in -k V0 -O $tmp"
+assert_no_diff $tmp $out.1
+clean
+
+run "$bp -I $in -k V0 -b 5 -O $tmp"
+assert_no_diff $tmp $out.2
+clean

diff --git a/code_ruby/Maasha/lib/biopieces.rb b/code_ruby/Maasha/lib/biopieces.rb
index 78a00505ed8ea72f0fd05b1a09974aad58991d25..2a4a9b2de3802392142cac5524b4d13440467379 100644 (file)
--- a/code_ruby/Maasha/lib/biopieces.rb
+++ b/code_ruby/Maasha/lib/biopieces.rb
@@ -256,7 +256,7 @@ end
 class OptionHandler
   REGEX_LIST   = /^(list|files|files!)$/
   REGEX_INT    = /^(int|uint)$/
-  REGEX_STRING = /^(string|file|file!|dir|dir!|genome)$/
+  REGEX_STRING = /^(file|file!|dir|dir!|genome)$/
 
   def initialize(argv, casts, script_path, test=nil)
     @argv        = argv
@@ -282,6 +282,10 @@ class OptionHandler
           option.on("-#{cast[:short]}", "--#{cast[:long]} F", Float) do |f|
             @options[cast[:long]] = f
           end
+        when 'string'
+          option.on("-#{cast[:short]}", "--#{cast[:long]} S", String) do |s|
+            @options[cast[:long]] = s.to_sym
+          end
         when REGEX_LIST
           option.on( "-#{cast[:short]}", "--#{cast[:long]} A", Array) do |a|
             @options[cast[:long]] = a

diff --git a/code_ruby/Maasha/test/test_biopieces.rb b/code_ruby/Maasha/test/test_biopieces.rb
index fdab1ac4ebbddc839574c2562b6fc39ea8b049ae..ec781d1955a8781a9854e15346d0844e4c018ce4 100755 (executable)
--- a/code_ruby/Maasha/test/test_biopieces.rb
+++ b/code_ruby/Maasha/test/test_biopieces.rb
@@ -236,7 +236,7 @@ class BiopiecesTest < Test::Unit::TestCase
     argv    = ["--foo", "bleh", "-I", DUMMY_FILE]
     casts   = [{:long=>"foo", :short=>"f", :type=>"string", :mandatory=>false, :default=>"bar", :allowed=>nil, :disallowed=>nil}]
     options = @bp.parse(argv, casts, SCRIPT_PATH)
-    assert_equal(options[:foo], "bleh")
+    assert_equal(options[:foo], "bleh".to_sym)
   end
 
   def test_Biopieces_parse_with_mandatory_cast_and_no_argument_raises