From 6cf36abfcc2b6e86f98a73483b12e781ba1cf9eb Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Wed, 10 Nov 2010 10:26:43 -0500
Subject: [PATCH] (recommit): porocessTaxonomynow removes parenthesis fixing
 various tree drawing issues in metagenomic tools. Major rework of MG tools
 needed to ensure reproducibility

---
 scripts/taxonomy/processTaxonomy.sh | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/scripts/taxonomy/processTaxonomy.sh b/scripts/taxonomy/processTaxonomy.sh
index 95c6c973a69..3c82f45776c 100755
--- a/scripts/taxonomy/processTaxonomy.sh
+++ b/scripts/taxonomy/processTaxonomy.sh
@@ -10,5 +10,9 @@ cat gi_taxid_nucl.dmp gi_taxid_prot.dmp > gi_taxid_all.dmp
 echo "Sorting gi2tax files..."
 sort -n -k 1 gi_taxid_all.dmp > gi_taxid_sorted.txt
 rm gi_taxid_nucl.dmp gi_taxid_prot.dmp gi_taxid_all.dmp
+echo "Removing parenthesis from names.dmp"
+cat names.dmp | sed s/\(/_/g | sed s/\)/_/g > names.temporary
+mv names.dmp names.dmp.orig
+mv names.temporary names.dmp