From dc7f1022b754a2bd00bff7ba62c09be3831aeac4 Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
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