From dd15f79bb95a118162a4e247a7c8689bd2f90e93 Mon Sep 17 00:00:00 2001
From: Hans <hansr@ethz.ch>
Date: Wed, 26 Apr 2023 09:23:12 +0200
Subject: [PATCH] Removed the bash careful mode as it created issues with
 Ubuntu users. Replaced a bash command for changing column orders in tabular
 files with a python script

---
 mOTUs-extender/extend_mOTUs_addGenome.sh      | 2 +-
 mOTUs-extender/extend_mOTUs_addMarkerGenes.sh | 2 +-
 mOTUs-extender/extend_mOTUs_generateDB.sh     | 5 +++--
 mOTUs-extender/swap_columns.py                | 6 ++++++
 4 files changed, 11 insertions(+), 4 deletions(-)
 create mode 100644 mOTUs-extender/swap_columns.py

diff --git a/mOTUs-extender/extend_mOTUs_addGenome.sh b/mOTUs-extender/extend_mOTUs_addGenome.sh
index c2ec879..12bbaf0 100755
--- a/mOTUs-extender/extend_mOTUs_addGenome.sh
+++ b/mOTUs-extender/extend_mOTUs_addGenome.sh
@@ -1,4 +1,4 @@
-set -euxo pipefail
+#set -euxo pipefail
 #add genomes to mOTU DB
 
 sequence_file=$1
diff --git a/mOTUs-extender/extend_mOTUs_addMarkerGenes.sh b/mOTUs-extender/extend_mOTUs_addMarkerGenes.sh
index 5f509a2..8490c0a 100755
--- a/mOTUs-extender/extend_mOTUs_addMarkerGenes.sh
+++ b/mOTUs-extender/extend_mOTUs_addMarkerGenes.sh
@@ -1,4 +1,4 @@
-set -euxo pipefail
+#set -euxo pipefail
 #add genomes to mOTU DB
 
 sequence_file=$1
diff --git a/mOTUs-extender/extend_mOTUs_generateDB.sh b/mOTUs-extender/extend_mOTUs_generateDB.sh
index c626b49..0e69a8d 100644
--- a/mOTUs-extender/extend_mOTUs_generateDB.sh
+++ b/mOTUs-extender/extend_mOTUs_generateDB.sh
@@ -1,4 +1,4 @@
-set -euxo pipefail
+#set -euxo pipefail
 #filter genomes from mOTU DB
 
 
@@ -155,7 +155,8 @@ do
 paste $new_database_folder/$newDBName/vsearch/$newDBName.mOTU-LG.map.tsv.temp1 $new_database_folder/$newDBName/vsearch/$newDBName.mOTU-LG.map.tsv.temp1 | sed "s/^/${line}./"
 done < $mOTU_MG_file > $new_database_folder/$newDBName/vsearch/$newDBName.mOTU-LG.map.tsv
 
-awk -F $'\t' ' { t = $1; $1 = $2; $2 = t; print; } ' OFS=$'\t' $new_database_folder/$newDBName/vsearch/$newDBName.mOTU-LG.map.tsv > $new_database_folder/$newDBName/vsearch/$newDBName.mOTU-LG.map.tsv.temp
+python $scriptDir/swap_columns.py $new_database_folder/$newDBName/vsearch/$newDBName.mOTU-LG.map.tsv > $new_database_folder/$newDBName/vsearch/$newDBName.mOTU-LG.map.tsv.temp
+#awk -F $'\t' ' { t = $1; $1 = $2; $2 = t; print; } ' OFS=$'\t' $new_database_folder/$newDBName/vsearch/$newDBName.mOTU-LG.map.tsv > $new_database_folder/$newDBName/vsearch/$newDBName.mOTU-LG.map.tsv.temp
 
 python $scriptDir/reformatMapping2Clustering.py $new_database_folder/$newDBName/vsearch/$newDBName.mOTU-LG.map.tsv.temp $new_database_folder/$newDBName/vsearch/$newDBName.mOTU-LG.map.line.tsv
 
diff --git a/mOTUs-extender/swap_columns.py b/mOTUs-extender/swap_columns.py
new file mode 100644
index 0000000..c84ac9a
--- /dev/null
+++ b/mOTUs-extender/swap_columns.py
@@ -0,0 +1,6 @@
+import sys
+
+with open(sys.argv[1]) as handle:
+    for line in handle:
+        splits = line.strip().split()
+        print(f'{splits[1]}\t{splits[0]}')