X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Fassemble_seq_velvet;h=98c0ba4486a23d47b6969cd9d56d2a4e1902f24b;hb=ed64328c7cb91daf65273e91be4bb373122798c4;hp=85c5fa81c4d3469108dd4a898cb9d37b88abbd43;hpb=0549ff0cda733c78853ec9039fa2b956b9f6a10b;p=biopieces.git

diff --git a/bp_bin/assemble_seq_velvet b/bp_bin/assemble_seq_velvet
index 85c5fa8..98c0ba4 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)
@@ -45,7 +45,7 @@ class Velvet
     kmer = @kmer_min
 
     while kmer <= @kmer_max
-      dir_velveth = [@directory, "Kmer_#{kmer}"].join(File::SEPARATOR)
+      dir_velveth = File.join(@directory, "Kmer_#{kmer}")
 
       Dir.mkdir(dir_velveth)
 
@@ -68,7 +68,7 @@ class Velvet
       files_velveth = Dir.glob("#{dir_velveth}/*")
 
       cov_cutoffs.each do |cov_cutoff|
-        dir_velvetg = [dir_velveth, "Cov_cutoff_#{cov_cutoff}"].join(File::SEPARATOR)
+        dir_velvetg = File.join(dir_velveth, "Cov_cutoff_#{cov_cutoff}")
 
         Dir.mkdir(dir_velvetg)
         FileUtils.cp_r files_velveth, dir_velvetg
@@ -148,11 +148,9 @@ casts << {:long=>'kmer_min',   :short=>'k', :type=>'uint',   :mandatory=>true,
 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}
+casts << {:long=>'clean',      :short=>'X', :type=>'flag',   :mandatory=>false, :default=>nil,         :allowed=>nil,   :disallowed=>nil}
 
-bp = Biopieces.new
-
-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?
@@ -160,25 +158,30 @@ raise ArgumentError, "kmer_min >= kmer_max: #{options[:kmer_min]} >= #{options[:
 
 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, mode="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[: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|
+				output.puts entry.to_bp
+			end
+		end
+	end
 end
 
 FileUtils.remove_entry_secure file_fasta