From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Wed, 9 Jan 2013 09:09:18 +0000 (+0000)
Subject: removed old assemle_seq_idba
X-Git-Url: https://git.donarmstrong.com/?p=biopieces.git;a=commitdiff_plain;h=e15fbd936563869452877d407f4635dac5e5b285

removed old assemle_seq_idba

git-svn-id: http://biopieces.googlecode.com/svn/trunk@2058 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/bp_bin/assemble_seq_idba b/bp_bin/assemble_seq_idba
deleted file mode 100755
index bd8b4a8..0000000
--- a/bp_bin/assemble_seq_idba
+++ /dev/null
@@ -1,128 +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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-# Assemble sequences in the stream using IDBA.
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-require 'maasha/biopieces'
-require 'maasha/fasta'
-
-casts = []
-casts << {:long=>'directory',  :short=>'d', :type=>'dir',  :mandatory=>true,  :default=>nil, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'scaffold',   :short=>'s', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'metagenome', :short=>'m', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'kmer_min',   :short=>'k', :type=>'uint', :mandatory=>false, :default=>25,  :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'kmer_max',   :short=>'K', :type=>'uint', :mandatory=>false, :default=>50,  :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'count_min',  :short=>'c', :type=>'uint', :mandatory=>false, :default=>2,   :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'cover',      :short=>'C', :type=>'uint', :mandatory=>false, :default=>0,   :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'pairs_min',  :short=>'p', :type=>'uint', :mandatory=>false, :default=>5,   :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'prefix_len', :short=>'P', :type=>'uint', :mandatory=>false, :default=>3,   :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'clean',      :short=>'X', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
-
-options = Biopieces.options_parse(ARGV, casts)
-
-Dir.mkdir(options[:directory]) unless Dir.exists?(options[:directory])
-
-file_fasta = File.join(options[:directory], "IDBA") + ".fna"
-
-count = 0
-
-Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
-	Fasta.open(file_fasta, mode="w") do |fasta_io|
-		input.each_record do |record|
-      if record[:SEQ_NAME] and record[:SEQ]
-        seq = Seq.new_bp(record)
-
-        if options[:scaffold] # we need to fix the sequence name for mate-pair IDBA
-          if seq.seq_name =~ /1$/
-            seq.seq_name = "read#{count}/1"
-          else
-            seq.seq_name = "read#{count}/2"
-
-            count += 1
-          end
-        end
-
-        fasta_io.puts seq.to_fasta
-      end
-		end
-	end
-
-	unless File.size(file_fasta) == 0
-		prefix = File.join(options[:directory], "IDBA")
-
-		commands = []
-		commands << "nice -n 19"
-
-    if options[:metagenome]
-		  commands << "metaidba"
-    else
-		  commands << "idba"
-    end
-
-		commands << "--read #{file_fasta}"
-		commands << "--output #{prefix}"
-		commands << "--scaffold" if options[:scaffold]
-		commands << "--mink #{options[:kmer_min]}"
-		commands << "--maxk #{options[:kmer_max]}"
-		commands << "--minCount #{options[:count_min]}"
-		commands << "--cover #{options[:cover]}"
-		commands << "--minPairs #{options[:pairs_min]}"
-		commands << "--prefixLength #{options[:prefix_len]}"
-		commands << "> /dev/null 2>&1" unless options[:verbose]
-
-		command = commands.join(" ")
-
-		begin
-			system(command)
-			raise "Command failed: #{command}" unless $?.success?
-		rescue
-			$stderr.puts "Command failed: #{command}"
-		end
-
-    if options[:scaffold]
-		  file_contig = File.join(options[:directory], "IDBA") + "-contig-mate.fa"
-    else
-		  file_contig = File.join(options[:directory], "IDBA") + "-contig.fa"
-    end
-
-		Fasta.open(file_contig, mode="r") do |fasta_io|
-			fasta_io.each do |entry|
-				output.puts entry.to_bp
-			end
-		end
-	end
-end
-
-FileUtils.remove_entry_secure file_fasta
-FileUtils.remove_entry_secure options[:directory] if options[:clean]
-
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-__END__