From 59f37cd460cb6580f465b243116ffe6c3ebe4d33 Mon Sep 17 00:00:00 2001 From: martinahansen Date: Wed, 4 May 2011 19:36:35 +0000 Subject: [PATCH] added assemble_seq_velvet draft biopiece git-svn-id: http://biopieces.googlecode.com/svn/trunk@1371 74ccb610-7750-0410-82ae-013aeee3265d --- bp_bin/assemble_seq_idba | 4 +- bp_bin/assemble_seq_velvet | 195 +++++++++++++++++++++++++++++++++++++ 2 files changed, 197 insertions(+), 2 deletions(-) create mode 100755 bp_bin/assemble_seq_velvet diff --git a/bp_bin/assemble_seq_idba b/bp_bin/assemble_seq_idba index 1fad90f..c1d72a2 100755 --- a/bp_bin/assemble_seq_idba +++ b/bp_bin/assemble_seq_idba @@ -49,7 +49,7 @@ options = bp.parse(ARGV, casts) Dir.mkdir(options[:directory]) unless Dir.exists?(options[:directory]) -file_fasta = [options[:directory], options[:name] ].join(File::SEPARATOR) + ".fna" +file_fasta = [options[:directory], options[:name]].join(File::SEPARATOR) + ".fna" Fasta.open(file_fasta, mode="w") do |fasta_io| bp.each_record do |record| @@ -58,7 +58,7 @@ Fasta.open(file_fasta, mode="w") do |fasta_io| end unless File.size(file_fasta) == 0 - output = [options[:directory], options[:name] ].join(File::SEPARATOR) + output = [options[:directory], options[:name]].join(File::SEPARATOR) commands = [] commands << "nice -n 19" diff --git a/bp_bin/assemble_seq_velvet b/bp_bin/assemble_seq_velvet new file mode 100755 index 0000000..cf6160f --- /dev/null +++ b/bp_bin/assemble_seq_velvet @@ -0,0 +1,195 @@ +#!/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__ -- 2.39.2