added scores_to_dec biopiece, wiki, and tests

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1075 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/scores_to_dec b/bp_bin/scores_to_dec
new file mode 100755 (executable)
index 0000000..9c94454
--- /dev/null
+++ b/bp_bin/scores_to_dec
@@ -0,0 +1,66 @@
+#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Convert ASCII encoded quality scores in stream to a semi-colon seperated string of decimal values.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+require 'biopieces'
+
+# Expading class Hash with possibly evil monkey patch.
+class Hash
+  # Method to convert scores from ASCII encode string to
+  # a semi-colon seperated string of decimal values.
+  def scores2dec!(base)
+    if self.has_key? :SCORES
+      self[:SCORES].gsub! /./ do |score|
+        score = (score.ord - base).to_s + ";"
+      end
+
+      self[:SCORES].chomp! ";"
+    end
+
+    self
+  end
+end
+
+casts = []
+casts << {:long=>'base', :short=>'b', :type=>'uint', :mandatory=>false, :default=>64, :allowed=>"33,59,64", :disallowed=>nil}
+
+bp = Biopieces.new
+
+options = bp.parse(ARGV, casts)
+
+bp.each_record do |record|
+  bp.puts record.scores2dec!(options[:base])
+end
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__

diff --git a/bp_test/in/scores_to_dec.in b/bp_test/in/scores_to_dec.in
new file mode 100644 (file)
index 0000000..e40bdf7
--- /dev/null
+++ b/bp_test/in/scores_to_dec.in
@@ -0,0 +1,2 @@
+SCORES: !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
+---

diff --git a/bp_test/out/scores_to_dec.out.1 b/bp_test/out/scores_to_dec.out.1
new file mode 100644 (file)
index 0000000..ddd77d4
--- /dev/null
+++ b/bp_test/out/scores_to_dec.out.1
@@ -0,0 +1,2 @@
+SCORES: -31;-30;-29;-28;-27;-26;-25;-24;-23;-22;-21;-20;-19;-18;-17;-16;-15;-14;-13;-12;-11;-10;-9;-8;-7;-6;-5;-4;-3;-2;-1;0;1;2;3;4;5;6;7;8;9;10;11;12;13;14;15;16;17;18;19;20;21;22;23;24;25;26;27;28;29;30;31;32;33;34;35;36;37;38;39;40;41;42;43;44;45;46;47;48;49;50;51;52;53;54;55;56;57;58;59;60;61;62
+---

diff --git a/bp_test/out/scores_to_dec.out.2 b/bp_test/out/scores_to_dec.out.2
new file mode 100644 (file)
index 0000000..00f19b6
--- /dev/null
+++ b/bp_test/out/scores_to_dec.out.2
@@ -0,0 +1,2 @@
+SCORES: 0;1;2;3;4;5;6;7;8;9;10;11;12;13;14;15;16;17;18;19;20;21;22;23;24;25;26;27;28;29;30;31;32;33;34;35;36;37;38;39;40;41;42;43;44;45;46;47;48;49;50;51;52;53;54;55;56;57;58;59;60;61;62;63;64;65;66;67;68;69;70;71;72;73;74;75;76;77;78;79;80;81;82;83;84;85;86;87;88;89;90;91;92;93
+---

diff --git a/bp_test/out/scores_to_dec.out.3 b/bp_test/out/scores_to_dec.out.3
new file mode 100644 (file)
index 0000000..c192097
--- /dev/null
+++ b/bp_test/out/scores_to_dec.out.3
@@ -0,0 +1,2 @@
+SCORES: -26;-25;-24;-23;-22;-21;-20;-19;-18;-17;-16;-15;-14;-13;-12;-11;-10;-9;-8;-7;-6;-5;-4;-3;-2;-1;0;1;2;3;4;5;6;7;8;9;10;11;12;13;14;15;16;17;18;19;20;21;22;23;24;25;26;27;28;29;30;31;32;33;34;35;36;37;38;39;40;41;42;43;44;45;46;47;48;49;50;51;52;53;54;55;56;57;58;59;60;61;62;63;64;65;66;67
+---

diff --git a/bp_test/test/test_scores_to_dec b/bp_test/test/test_scores_to_dec
new file mode 100755 (executable)
index 0000000..d4e7076
--- /dev/null
+++ b/bp_test/test/test_scores_to_dec
@@ -0,0 +1,15 @@
+#!/bin/bash
+
+source "$BP_DIR/bp_test/lib/test.sh"
+
+run "$bp -I $in -O $tmp"
+assert_no_diff $tmp $out.1
+clean
+
+run "$bp -I $in -b 33 -O $tmp"
+assert_no_diff $tmp $out.2
+clean
+
+run "$bp -I $in -b 59 -O $tmp"
+assert_no_diff $tmp $out.3
+clean