From 6b7e0532884d683d9908f53da7eb7f6ba0b029c0 Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Thu, 16 Dec 2010 11:08:25 +0000
Subject: [PATCH] added find_homopolymers biopiece

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1189 74ccb610-7750-0410-82ae-013aeee3265d
---
 bp_bin/find_homopolymers            | 56 +++++++++++++++++++++++++++++
 bp_test/in/find_homopolymers.in     | 16 +++++++++
 bp_test/out/find_homopolymers.out.1 | 20 +++++++++++
 bp_test/test/test_find_homopolymers |  7 ++++
 code_ruby/Maasha/lib/seq.rb         | 14 ++++++++
 code_ruby/Maasha/test/test_seq.rb   | 15 ++++++++
 6 files changed, 128 insertions(+)
 create mode 100755 bp_bin/find_homopolymers
 create mode 100644 bp_test/in/find_homopolymers.in
 create mode 100644 bp_test/out/find_homopolymers.out.1
 create mode 100755 bp_test/test/test_find_homopolymers

diff --git a/bp_bin/find_homopolymers b/bp_bin/find_homopolymers
new file mode 100755
index 0000000..097d651
--- /dev/null
+++ b/bp_bin/find_homopolymers
@@ -0,0 +1,56 @@
+#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Find homopolymers in sequences in the stream.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+require 'biopieces'
+require 'seq'
+require 'pp'
+
+casts = []
+
+bp = Biopieces.new
+
+options = bp.parse(ARGV, casts)
+
+bp.each_record do |record|
+  if record.has_key? :SEQ
+    seq = Seq.new(nil, record[:SEQ])
+
+    record[:HOMOPOL_MAX] = seq.homopol_max
+  end
+
+  bp.puts record
+end
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__
diff --git a/bp_test/in/find_homopolymers.in b/bp_test/in/find_homopolymers.in
new file mode 100644
index 0000000..1259c9c
--- /dev/null
+++ b/bp_test/in/find_homopolymers.in
@@ -0,0 +1,16 @@
+SEQ_NAME: test1
+SEQ: attcccggggnnnnn
+SEQ_LEN: 15
+---
+SEQ_NAME: test2
+SEQ: nnnnnggggccctta
+SEQ_LEN: 15
+---
+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.1 b/bp_test/out/find_homopolymers.out.1
new file mode 100644
index 0000000..fcd0ce9
--- /dev/null
+++ b/bp_test/out/find_homopolymers.out.1
@@ -0,0 +1,20 @@
+SEQ_NAME: test1
+SEQ: attcccggggnnnnn
+SEQ_LEN: 15
+HOMOPOL_MAX: 5
+---
+SEQ_NAME: test2
+SEQ: nnnnnggggccctta
+SEQ_LEN: 15
+HOMOPOL_MAX: 5
+---
+SEQ_NAME: test3
+SEQ: a
+SEQ_LEN: 1
+HOMOPOL_MAX: 1
+---
+SEQ_NAME: test4
+SEQ: aA
+SEQ_LEN: 2
+HOMOPOL_MAX: 2
+---
diff --git a/bp_test/test/test_find_homopolymers b/bp_test/test/test_find_homopolymers
new file mode 100755
index 0000000..61c5709
--- /dev/null
+++ b/bp_test/test/test_find_homopolymers
@@ -0,0 +1,7 @@
+#!/bin/bash
+
+source "$BP_DIR/bp_test/lib/test.sh"
+
+run "$bp -I $in -O $tmp"
+assert_no_diff $tmp $out.1
+clean
diff --git a/code_ruby/Maasha/lib/seq.rb b/code_ruby/Maasha/lib/seq.rb
index 4c28292..a6f071d 100644
--- a/code_ruby/Maasha/lib/seq.rb
+++ b/code_ruby/Maasha/lib/seq.rb
@@ -162,6 +162,20 @@ class Seq
     comp
   end
 
+  # Method that returns the length of the longest homopolymeric stretch
+  # found in a sequence.
+  def homopol_max
+    max = 0
+
+    if self.seq
+      self.seq.upcase.scan(/[A]+|[T]+|[G]+|[C]+|[N]+/) do |match|
+        max = [match.size, max].max
+      end
+    end
+
+    max
+  end
+
   # Method that returns the percentage of hard masked residues
   # or N's in a sequence.
   def hard_mask
diff --git a/code_ruby/Maasha/test/test_seq.rb b/code_ruby/Maasha/test/test_seq.rb
index de60d4c..a5a2732 100755
--- a/code_ruby/Maasha/test/test_seq.rb
+++ b/code_ruby/Maasha/test/test_seq.rb
@@ -191,6 +191,21 @@ class TestSeq < Test::Unit::TestCase
     assert_equal(0, @entry.composition["X"])
   end
 
+  def test_Seq_homopol_max_returns_0_with_empty_sequence
+    @entry.seq = ""
+    assert_equal(0, @entry.homopol_max)
+  end
+
+  def test_Seq_homopol_max_returns_0_with_nil_sequence
+    @entry.seq = nil
+    assert_equal(0, @entry.homopol_max)
+  end
+
+  def test_Seq_homopol_max_returns_correctly
+    @entry.seq = "AtTcCcGggGnnNnn"
+    assert_equal(5, @entry.homopol_max)
+  end
+
   def test_Seq_hard_mask_returns_correctly
     @entry.seq = "--AAAANn"
     assert_equal(33.33, @entry.hard_mask)
-- 
2.39.5