--- /dev/null
+#!/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 Velvet.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+require 'biopieces'
+require 'fasta'
+require 'pp'
+
+class Velvet
+ def initialize(directory, sequence_file, verbose)
+ @directory = directory
+ @sequence_file = sequence_file
+ @verbose = verbose
+ end
+
+ def run_velveth(kmer_min, kmer_max, type)
+ @kmer_min = kmer_min
+ @kmer_max = kmer_max
+
+ kmer = @kmer_min
+
+ while kmer <= @kmer_max
+ dir_velveth = [@directory, "Velvet_#{kmer}"].join(File::SEPARATOR)
+
+ Dir.mkdir(dir_velveth)
+
+ commands = []
+ commands << "velveth"
+ commands << dir_velveth
+ commands << kmer
+ commands << "-#{type}"
+ commands << "-fasta"
+ commands << @sequence_file
+
+ execute(commands)
+
+ kmer += 2
+ end
+ end
+
+ def run_velvetg(cov_cutoffs, exp_cov)
+ Dir.glob("#{@directory}/Velvet_*").each do |dir_velveth|
+ files_velveth = Dir.glob("#{dir_velveth}/*")
+
+ cov_cutoffs.each do |cov_cutoff|
+ dir_velvetg = [dir_velveth, "Cov_cutoff_#{cov_cutoff}"].join(File::SEPARATOR)
+
+ Dir.mkdir(dir_velvetg)
+ FileUtils.cp_r files_velveth, dir_velvetg
+
+ commands = []
+ commands << "velvetg"
+ commands << dir_velvetg
+ commands << "-cov_cutoff #{cov_cutoff}"
+ commands << "-exp_cov #{exp_cov}"
+
+ execute(commands)
+ end
+ end
+ end
+
+ def pick_best_assembly
+ list = []
+
+ Dir.glob("#{@directory}/Velvet_*/Cov_cutoff_*/contigs.fa").each do |file|
+ n50 = fasta_n50(file)
+ list << [file, n50]
+ end
+
+ list.sort_by { |e| e.last }.last.first
+ end
+
+ private
+
+ def execute(commands)
+ commands.unshift "nice -n 19"
+ commands.push "> /dev/null 2>&1" unless @verbose
+
+ command = commands.join(" ")
+
+ begin
+ system(command)
+ raise "Command failed: #{command}" unless $?.success?
+ rescue
+ $stderr.puts "Command failed: #{command}"
+ end
+ end
+
+ def fasta_n50(file)
+ total = 0
+ lengths = []
+
+ Fasta.open(file, mode="r") do |fasta_io|
+ fasta_io.each do |entry|
+ total += entry.length
+ lengths << entry.length
+ end
+ end
+
+ n50(total, lengths)
+ end
+
+ def n50(total, lengths)
+ count = 0
+ n50 = 0
+
+ lengths.sort.reverse.each do |length|
+ count += length
+
+ if count >= total * 0.50
+ n50 = length
+ break
+ end
+ end
+
+ n50
+ end
+end
+
+types = 'short,shortPaired,long,longPaired'
+cov_cutoffs = "2,4,8,16"
+
+casts = []
+casts << {:long=>'directory', :short=>'d', :type=>'dir', :mandatory=>true, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'type', :short=>'t', :type=>'string', :mandatory=>true, :default=>'short', :allowed=>types, :disallowed=>nil}
+casts << {:long=>'kmer_min', :short=>'k', :type=>'uint', :mandatory=>true, :default=>19, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'kmer_max', :short=>'K', :type=>'uint', :mandatory=>true, :default=>31, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'cov_cutoff', :short=>'c', :type=>'list', :mandatory=>true, :default=>cov_cutoffs, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'exp_cov', :short=>'e', :type=>'float', :mandatory=>true, :default=>'auto', :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'clean', :short=>'x', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+
+bp = Biopieces.new
+
+options = bp.parse(ARGV, casts)
+
+raise ArgumentError, "kmer_min #{options[:kmer_min]} must be uneven." if options[:kmer_min].even?
+raise ArgumentError, "kmer_max #{options[:kmer_max]} must be uneven." if options[:kmer_max].even?
+raise ArgumentError, "kmer_min >= kmer_max: #{options[:kmer_min]} >= #{options[:kmer_max]}" unless options[:kmer_max] > options[:kmer_min]
+
+Dir.mkdir(options[:directory]) unless Dir.exists?(options[:directory])
+
+file_fasta = [options[:directory], "sequence_in.fna"].join(File::SEPARATOR)
+
+Fasta.open(file_fasta, mode="w") do |fasta_io|
+ bp.each_record do |record|
+ fasta_io.puts record
+ end
+end
+
+unless File.size(file_fasta) == 0
+ velvet = Velvet.new(options[:directory], file_fasta, options[:verbose])
+ velvet.run_velveth(options[:kmer_min], options[:kmer_max], options[:type])
+ velvet.run_velvetg(options[:cov_cutoff], options[:exp_cov])
+ file_contigs = velvet.pick_best_assembly
+
+ Fasta.open(file_contigs, mode="r") do |fasta_io|
+ fasta_io.each do |entry|
+ bp.puts entry.to_bp
+ end
+ end
+end
+
+FileUtils.remove_entry_secure options[:directory] if options[:clean]
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__
projects / biopieces.git / commitdiff