From c222afd992571690e833d37a6db05cc6c4a0840b Mon Sep 17 00:00:00 2001
From: caleb <caleb.easterly@gmail.com>
Date: Thu, 2 Nov 2017 13:17:02 -0500
Subject: [PATCH] add flag to automatically overwrite when decompressing

---
 download_eggnog_data.py | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/download_eggnog_data.py b/download_eggnog_data.py
index 26226b82..dd75d8d8 100755
--- a/download_eggnog_data.py
+++ b/download_eggnog_data.py
@@ -11,6 +11,13 @@ def run(cmd):
     if not args.simulate:
         os.system(cmd)
 
+def gunzip_flag():
+    if args.force:
+        return '-f'
+    else:
+        return ''
+
+
 def download_hmm_database(level):
     level_base_path = get_level_base_path(level)
     target_dir = os.path.split(get_db_info(level)[0])[0]
@@ -27,7 +34,7 @@ def download_hmm_database(level):
 
 def download_annotations():
     url = 'http://eggnogdb.embl.de/download/emapperdb-%s/eggnog.db.gz' %(DATABASE_VERSION)
-    cmd = 'cd %s && wget -nH --user-agent=Mozilla/5.0 --relative --no-parent --reject "index.html*" --cut-dirs=4 -e robots=off -O eggnog.db.gz %s && echo Decompressing... && gunzip eggnog.db.gz' %(get_data_path(), url)
+    cmd = 'cd %s && wget -nH --user-agent=Mozilla/5.0 --relative --no-parent --reject "index.html*" --cut-dirs=4 -e robots=off -O eggnog.db.gz %s && echo Decompressing... && gunzip eggnog.db.gz %s' %(get_data_path(), url, gunzip_flag())
     run(cmd)
 
 def download_groups():
@@ -37,7 +44,7 @@ def download_groups():
 
 def download_diamond_db():
     url = 'http://eggnogdb.embl.de/download/emapperdb-%s/eggnog_proteins.dmnd.gz' %(DATABASE_VERSION)
-    cmd = 'cd %s && wget -nH --user-agent=Mozilla/5.0 --relative --no-parent --reject "index.html*" --cut-dirs=4 -e robots=off -O eggnog_proteins.dmnd.gz  %s && echo Decompressing... && gunzip eggnog_proteins.dmnd.gz' %(get_data_path(),  url)
+    cmd = 'cd %s && wget -nH --user-agent=Mozilla/5.0 --relative --no-parent --reject "index.html*" --cut-dirs=4 -e robots=off -O eggnog_proteins.dmnd.gz  %s && echo Decompressing... && gunzip eggnog_proteins.dmnd.gz %s' %(get_data_path(),  url, gunzip_flag())
     run(cmd)
 
 def download_og2level():