added missing files

git-svn-id: http://biopieces.googlecode.com/svn/trunk@2176 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_test/out/find_homopolymers.out.3 b/bp_test/out/find_homopolymers.out.3
new file mode 100644 (file)
index 0000000..740c170
--- /dev/null
+++ b/bp_test/out/find_homopolymers.out.3
@@ -0,0 +1,22 @@
+SEQ_NAME: test1
+SEQ: attcccggggnnnnn
+SEQ_LEN: 15
+HOMOPOL_PAT: CCC
+HOMOPOL_LEN: 3
+HOMOPOL_POS: 3
+---
+SEQ_NAME: test2
+SEQ: nnnnnggggccctta
+SEQ_LEN: 15
+HOMOPOL_PAT: NNNNN
+HOMOPOL_LEN: 5
+HOMOPOL_POS: 0
+---
+SEQ_NAME: test3
+SEQ: a
+SEQ_LEN: 1
+---
+SEQ_NAME: test4
+SEQ: aA
+SEQ_LEN: 2
+---

diff --git a/bp_test/out/find_homopolymers.out.4 b/bp_test/out/find_homopolymers.out.4
new file mode 100644 (file)
index 0000000..27f9400
--- /dev/null
+++ b/bp_test/out/find_homopolymers.out.4
@@ -0,0 +1,22 @@
+SEQ_NAME: test1
+SEQ: attcccggggnnnnn
+SEQ_LEN: 15
+HOMOPOL_PAT: NNNNN
+HOMOPOL_LEN: 5
+HOMOPOL_POS: 10
+---
+SEQ_NAME: test2
+SEQ: nnnnnggggccctta
+SEQ_LEN: 15
+HOMOPOL_PAT: NNNNN
+HOMOPOL_LEN: 5
+HOMOPOL_POS: 0
+---
+SEQ_NAME: test3
+SEQ: a
+SEQ_LEN: 1
+---
+SEQ_NAME: test4
+SEQ: aA
+SEQ_LEN: 2
+---

diff --git a/code_ruby/lib/maasha/seq/homopolymer.rb b/code_ruby/lib/maasha/seq/homopolymer.rb
new file mode 100644 (file)
index 0000000..9aa46eb
--- /dev/null
+++ b/code_ruby/lib/maasha/seq/homopolymer.rb
@@ -0,0 +1,55 @@
+# Copyright (C) 2007-2013 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 software is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+module Homopolymer
+  # Error class for all exceptions to do with Homopolymer.
+  class HomopolymerError < StandardError; end
+
+  def each_homopolymer(min = 1)
+    list = []
+
+    self.seq.upcase.scan(/A{#{min},}|T{#{min},}|G{#{min},}|C{#{min},}|N{#{min},}/) do |match|
+      hp = Homopolymer.new(match, match.length, $`.length)
+
+      if block_given?
+        yield hp
+      else
+        list << hp
+      end
+    end
+
+    block_given? ? self : list
+  end
+
+  class Homopolymer
+    attr_reader :pattern, :length, :pos
+
+    def initialize(pattern, length, pos)
+      @pattern = pattern
+      @length  = length
+      @pos     = pos
+    end
+  end
+end

diff --git a/code_ruby/test/maasha/seq/test_homopolymer.rb b/code_ruby/test/maasha/seq/test_homopolymer.rb
new file mode 100755 (executable)
index 0000000..a574fd8
--- /dev/null
+++ b/code_ruby/test/maasha/seq/test_homopolymer.rb
@@ -0,0 +1,68 @@
+#!/usr/bin/env ruby
+$:.unshift File.join(File.dirname(__FILE__), '..', '..', '..')
+
+# Copyright (C) 2007-2013 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 software is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+require 'test/unit'
+require 'test/helper'
+require 'maasha/seq'
+
+class HomopolymerTest < Test::Unit::TestCase
+  def setup
+    #                         0         1
+    #                         01234567890123456789
+    @entry = Seq.new("test", "tacgatgctagcatgcacgg")
+    @entry.extend(Homopolymer)
+  end
+
+  test "#each_homopolymer returns empty with empty sequence" do
+    @entry.seq = ""
+    assert_equal([], @entry.each_homopolymer)
+  end
+
+  test "#each_homopolymer returns empty when none found" do
+    @entry.seq = "AtTcCcGggGnnNnn"
+    assert_equal([], @entry.each_homopolymer(6))
+  end
+
+  test "#each_homopolymer returns correctly" do
+    @entry.seq = "AtTcCcGggGnnNnn"
+    assert_equal('CCC', @entry.each_homopolymer(3).first.pattern)
+    assert_equal(3,     @entry.each_homopolymer(3).first.pos)
+    assert_equal(3,     @entry.each_homopolymer(3).first.length)
+  end
+
+  test "#each_homopolymer in block context returns correctly" do
+    @entry.seq = "AtTcCcGggGnnNnn"
+
+    @entry.each_homopolymer(3) do |hp|
+      assert_equal('CCC', hp.pattern)
+      assert_equal(3,     hp.pos)
+      assert_equal(3,     hp.length)
+
+      break
+    end
+  end
+end