From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Mon, 31 Jan 2011 20:46:20 +0000 (+0000)
Subject: remove calc_n50
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=117833b82ff50e323868676979960cd6e6d243ed;p=biopieces.git

remove calc_n50

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1237 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/bp_bin/calc_n50 b/bp_bin/calc_n50
deleted file mode 100755
index 3b7d4e4..0000000
--- a/bp_bin/calc_n50
+++ /dev/null
@@ -1,71 +0,0 @@
-#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-# Calculate n50 for sequences in the stream.
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-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
-
-bp.out = Stream.write(options[:data_out])
-
-count = 0
-
-lengths.sort.reverse.each do |length|
-  count += length
-
-  if count >= total * 0.50
-    bp.puts "N50" => length
-    break
-  end
-end
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-__END__