From 0be23a86e418adce44df86123d17ea5a9552e369 Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Tue, 1 Feb 2011 13:55:08 +0000
Subject: [PATCH] added analyze_assembly biopiece

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1247 74ccb610-7750-0410-82ae-013aeee3265d
---
 bp_bin/analyze_assembly            | 82 ++++++++++++++++++++++++++++++
 bp_test/in/analyze_assembly.in     | 20 ++++++++
 bp_test/out/analyze_assembly.out.1 | 27 ++++++++++
 bp_test/out/analyze_assembly.out.2 |  7 +++
 bp_test/test/test_analyze_assembly | 11 ++++
 5 files changed, 147 insertions(+)
 create mode 100755 bp_bin/analyze_assembly
 create mode 100644 bp_test/in/analyze_assembly.in
 create mode 100644 bp_test/out/analyze_assembly.out.1
 create mode 100644 bp_test/out/analyze_assembly.out.2
 create mode 100755 bp_test/test/test_analyze_assembly

diff --git a/bp_bin/analyze_assembly b/bp_bin/analyze_assembly
new file mode 100755
index 0000000..610d7e1
--- /dev/null
+++ b/bp_bin/analyze_assembly
@@ -0,0 +1,82 @@
+#!/usr/bin/env ruby
+
+# Copyright (C) 2007-2011 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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Analyze assembled sequences in the stream and output stats.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+require 'biopieces'
+require 'pp'
+
+casts = []
+casts << {:long=>'no_stream', :short=>'x', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'data_out',  :short=>'o', :type=>'file', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+
+bp = Biopieces.new
+
+options = bp.parse(ARGV, casts)
+
+total   = 0
+lengths = []
+
+bp.each_record do |record|
+  bp.puts record unless options[:no_stream]
+
+  if record.has_key? :SEQ
+    total   += record[:SEQ].length
+    lengths << record[:SEQ].length
+  end
+end
+
+count = 0
+n50   = 0
+
+lengths.sort.reverse.each do |length|
+  count += length
+
+  if count >= total * 0.50
+    n50 = length
+    break
+  end
+end
+
+bp.out = Stream.write(options[:data_out]) if options[:data_out]
+
+new_record = {}
+new_record[:N50]   = n50
+new_record[:MAX]   = lengths.max
+new_record[:MIN]   = lengths.min
+new_record[:MEAN]  = (total.to_f / lengths.size.to_f).to_i
+new_record[:TOTAL] = total
+new_record[:COUNT] = lengths.size
+
+bp.puts new_record
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__
diff --git a/bp_test/in/analyze_assembly.in b/bp_test/in/analyze_assembly.in
new file mode 100644
index 0000000..b973713
--- /dev/null
+++ b/bp_test/in/analyze_assembly.in
@@ -0,0 +1,20 @@
+SEQ_NAME: test1
+SEQ: ATGCACATTG
+SEQ_LEN: 10
+---
+SEQ_NAME: test2
+SEQ: ATGCACATTGATGCACATTG
+SEQ_LEN: 20
+---
+SEQ_NAME: test3
+SEQ: ATGCACATTGATGCACATTGATGCACATTG
+SEQ_LEN: 30
+---
+SEQ_NAME: test4
+SEQ: ATGCACATTGATGCACATTGATGCACATTGATGCACATTG
+SEQ_LEN: 40
+---
+SEQ_NAME: test5
+SEQ: ATGCACATTGATGCACATTGATGCACATTGATGCACATTGATGCACATTG
+SEQ_LEN: 50
+---
diff --git a/bp_test/out/analyze_assembly.out.1 b/bp_test/out/analyze_assembly.out.1
new file mode 100644
index 0000000..c47d842
--- /dev/null
+++ b/bp_test/out/analyze_assembly.out.1
@@ -0,0 +1,27 @@
+SEQ_NAME: test1
+SEQ: ATGCACATTG
+SEQ_LEN: 10
+---
+SEQ_NAME: test2
+SEQ: ATGCACATTGATGCACATTG
+SEQ_LEN: 20
+---
+SEQ_NAME: test3
+SEQ: ATGCACATTGATGCACATTGATGCACATTG
+SEQ_LEN: 30
+---
+SEQ_NAME: test4
+SEQ: ATGCACATTGATGCACATTGATGCACATTGATGCACATTG
+SEQ_LEN: 40
+---
+SEQ_NAME: test5
+SEQ: ATGCACATTGATGCACATTGATGCACATTGATGCACATTGATGCACATTG
+SEQ_LEN: 50
+---
+N50: 40
+MAX: 50
+MIN: 10
+MEAN: 30
+TOTAL: 150
+COUNT: 5
+---
diff --git a/bp_test/out/analyze_assembly.out.2 b/bp_test/out/analyze_assembly.out.2
new file mode 100644
index 0000000..d10623b
--- /dev/null
+++ b/bp_test/out/analyze_assembly.out.2
@@ -0,0 +1,7 @@
+N50: 40
+MAX: 50
+MIN: 10
+MEAN: 30
+TOTAL: 150
+COUNT: 5
+---
diff --git a/bp_test/test/test_analyze_assembly b/bp_test/test/test_analyze_assembly
new file mode 100755
index 0000000..20dfa3d
--- /dev/null
+++ b/bp_test/test/test_analyze_assembly
@@ -0,0 +1,11 @@
+#!/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 -o $tmp -x"
+assert_no_diff $tmp $out.2
+clean
-- 
2.39.2