From 6c1d90a31caa1fe54bedc965ba26940688a31ab0 Mon Sep 17 00:00:00 2001 From: martinahansen Date: Wed, 18 Dec 2013 17:16:12 +0000 Subject: [PATCH] updateing to idba hybrid git-svn-id: http://biopieces.googlecode.com/svn/trunk@2279 74ccb610-7750-0410-82ae-013aeee3265d --- bp_bin/assemble_seq_idba | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/bp_bin/assemble_seq_idba b/bp_bin/assemble_seq_idba index 87b81a2..fcf13f8 100755 --- a/bp_bin/assemble_seq_idba +++ b/bp_bin/assemble_seq_idba @@ -24,7 +24,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< -# Assemble sequences in the stream using IDBA-UD. +# Assemble sequences in the stream using idba hybrid. # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< @@ -38,14 +38,14 @@ casts << {:long=>'kmer_max', :short=>'K', :type=>'uint', :mandatory=>false, :d casts << {:long=>'count_min', :short=>'c', :type=>'uint', :mandatory=>false, :default=>2, :allowed=>nil, :disallowed=>nil} casts << {:long=>'pairs_min', :short=>'p', :type=>'uint', :mandatory=>false, :default=>3, :allowed=>nil, :disallowed=>nil} casts << {:long=>'prefix_len', :short=>'P', :type=>'uint', :mandatory=>false, :default=>3, :allowed=>nil, :disallowed=>nil} -casts << {:long=>'cpus', :short=>'C', :type=>'uint', :mandatory=>false, :default=>0, :allowed=>nil, :disallowed=>nil} +casts << {:long=>'cpus', :short=>'C', :type=>'uint', :mandatory=>false, :default=>1, :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-UD") + ".fna" +file_fasta = File.join(options[:directory], "IDBA-HYBRID") + ".fna" count = 0 @@ -61,11 +61,10 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output| end unless File.size(file_fasta) == 0 - prefix = File.join(options[:directory], "IDBA-UD") + prefix = File.join(options[:directory], "IDBA-HYBRID") commands = [] - commands << "nice -n 19" - commands << "idba_ud" + commands << "idba_hybrid" commands << "--read #{file_fasta}" commands << "--out #{prefix}" commands << "--mink #{options[:kmer_min]}" @@ -81,7 +80,7 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output| system(command) raise "Command failed: #{command}" unless $?.success? - file_contig = File.join(options[:directory], "IDBA-UD", "contig.fa") + file_contig = File.join(options[:directory], "IDBA-HYBRID", "contig.fa") Fasta.open(file_contig, "r") do |fasta_io| fasta_io.each do |entry| -- 2.39.2