X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Fassemble_seq_velvet;h=e2753ce91ad65023d47627bd1c372553075fb14e;hb=2f0fd91b461033529a4a72e161bd133252a22eb6;hp=85c5fa81c4d3469108dd4a898cb9d37b88abbd43;hpb=0549ff0cda733c78853ec9039fa2b956b9f6a10b;p=biopieces.git

diff --git a/bp_bin/assemble_seq_velvet b/bp_bin/assemble_seq_velvet
index 85c5fa8..e2753ce 100755
--- a/bp_bin/assemble_seq_velvet
+++ b/bp_bin/assemble_seq_velvet
@@ -28,8 +28,8 @@
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
-require 'biopieces'
-require 'fasta'
+require 'maasha/biopieces'
+require 'maasha/fasta'
 
 class Velvet
   def initialize(directory, sequence_file, verbose)
@@ -38,57 +38,40 @@ class Velvet
     @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, "Kmer_#{kmer}"].join(File::SEPARATOR)
+  def run_velveth(kmer_min, kmer_max, kmer_step, type)
+    commands = []
+    commands << "velveth"
+    commands << @directory + File::SEPARATOR
+    commands << "#{kmer_min},#{kmer_max + kmer_step},#{kmer_step}"   # FIXME - ugly fix for velvet bug
+    commands << "-create_binary"
+    commands << "-#{type}"
+    commands << "-fasta"
+    commands << @sequence_file
+
+    execute(commands)
+  end
 
-      Dir.mkdir(dir_velveth)
+  def run_velvetg(ins_length, paired)
+    dirs = Dir.entries(@directory).select { |d| d.match(/^_/) }
 
+    dirs.each do |dir|
       commands = []
-      commands << "velveth"
-      commands << dir_velveth
-      commands << kmer
-      commands << "-#{type}"
-      commands << "-fasta"
-      commands << @sequence_file
+      commands << "velvetg"
+      commands << File.join(@directory, dir)
+      commands << "-cov_cutoff auto"
+      commands << "-exp_cov auto"
+      commands << "-ins_length #{ins_length}" if paired
+      commands << "-clean yes"
+      commands << "-min_contig_lgth 200"
 
       execute(commands)
-
-      kmer += 2
-    end
-  end
-
-  def run_velvetg(cov_cutoffs, exp_cov)
-    Dir.glob("#{@directory}/Kmer_*").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}"
-        commands << "-clean yes"
-
-        execute(commands)
-      end
     end
   end
 
   def pick_best_assembly
     list = []
 
-    Dir.glob("#{@directory}/Kmer_*/Cov_cutoff_*/contigs.fa").each do |file|
+    Dir.glob("#{@directory}/_*/contigs.fa").each do |file|
       n50 = fasta_n50(file)
       list << [file, n50]
     end
@@ -99,12 +82,12 @@ class Velvet
   private
 
   def execute(commands)
-    commands.unshift "nice -n 19"
     commands.push "> /dev/null 2>&1" unless @verbose
 
     command = commands.join(" ")
 
     begin
+      $stderr.puts command if @verbose
       system(command)
       raise "Command failed: #{command}" unless $?.success?
     rescue
@@ -118,7 +101,7 @@ class Velvet
     count   = 0
     n50     = 0
 
-    Fasta.open(file, mode="r") do |fasta_io|
+    Fasta.open(file, "r") do |fasta_io|
       fasta_io.each do |entry|
         total   += entry.length
         lengths << entry.length
@@ -138,53 +121,58 @@ class Velvet
   end
 end
 
-types       = 'short,shortPaired,long,longPaired'
-cov_cutoffs = "2,4,8,16"
+types = 'short,shortPaired,long,longPaired'
 
 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
+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=>'kmer_step',  :short=>'s', :type=>'uint',   :mandatory=>true,  :default=>2,       :allowed=>nil,   :disallowed=>nil}
+casts << {:long=>'ins_length', :short=>'i', :type=>'uint',   :mandatory=>false, :default=>nil,     :allowed=>nil,   :disallowed=>nil}
+casts << {:long=>'clean',      :short=>'X', :type=>'flag',   :mandatory=>false, :default=>nil,     :allowed=>nil,   :disallowed=>nil}
 
-options = bp.parse(ARGV, casts)
+options = Biopieces.options_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_step #{options[:kmer_step]} must be even." unless options[:kmer_step].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
+file_fasta = File.join(options[:directory], "sequence_in.fna")
 
-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
+Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
+  Fasta.open(file_fasta, "w") do |fasta_io|
+    input.each_record do |record|
+      if record[:SEQ_NAME] and record[:SEQ]
+        seq = Seq.new_bp(record)
+        fasta_io.puts seq.to_fasta
+      end
     end
-  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[:kmer_step], options[:type])
+		velvet.run_velvetg(options[:ins_length], options[:type].match("Paired"))
+		file_contigs = velvet.pick_best_assembly
+
+    kmer = file_contigs.match(/_\d+/)
+
+		Fasta.open(file_contigs, "r") do |fasta_io|
+		  fasta_io.each do |entry|
+        entry.seq_name << "_kmer#{kmer}"
+			  output.puts entry.to_bp
+	    end
+		end
+ 	end
 end
 
 FileUtils.remove_entry_secure file_fasta
 FileUtils.remove_entry_secure options[:directory] if options[:clean]
 
-
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<