From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Mon, 31 Oct 2011 13:36:44 +0000 (+0000)
Subject: added metagenome flag to assemble_seq_idba
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=dc7f1022b754a2bd00bff7ba62c09be3831aeac4;p=biopieces.git

added metagenome flag to assemble_seq_idba

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1605 74ccb610-7750-0410-82ae-013aeee3265d
---

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]