From dc7f1022b754a2bd00bff7ba62c09be3831aeac4 Mon Sep 17 00:00:00 2001 From: martinahansen Date: Mon, 31 Oct 2011 13:36:44 +0000 Subject: [PATCH] added metagenome flag to assemble_seq_idba git-svn-id: http://biopieces.googlecode.com/svn/trunk@1605 74ccb610-7750-0410-82ae-013aeee3265d --- bp_bin/assemble_seq_idba | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/bp_bin/assemble_seq_idba b/bp_bin/assemble_seq_idba index 2b65543..bd8b4a8 100755 --- a/bp_bin/assemble_seq_idba +++ b/bp_bin/assemble_seq_idba @@ -34,6 +34,7 @@ require 'maasha/fasta' casts = [] casts << {:long=>'directory', :short=>'d', :type=>'dir', :mandatory=>true, :default=>nil, :allowed=>nil, :disallowed=>nil} casts << {:long=>'scaffold', :short=>'s', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil} +casts << {:long=>'metagenome', :short=>'m', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil} casts << {:long=>'kmer_min', :short=>'k', :type=>'uint', :mandatory=>false, :default=>25, :allowed=>nil, :disallowed=>nil} casts << {:long=>'kmer_max', :short=>'K', :type=>'uint', :mandatory=>false, :default=>50, :allowed=>nil, :disallowed=>nil} casts << {:long=>'count_min', :short=>'c', :type=>'uint', :mandatory=>false, :default=>2, :allowed=>nil, :disallowed=>nil} @@ -76,7 +77,13 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output| commands = [] commands << "nice -n 19" - commands << "idba" + + if options[:metagenome] + commands << "metaidba" + else + commands << "idba" + end + commands << "--read #{file_fasta}" commands << "--output #{prefix}" commands << "--scaffold" if options[:scaffold] -- 2.39.5