From da2cd5a32d88e15154824b58a584ec061305c028 Mon Sep 17 00:00:00 2001 From: VinzentRisch Date: Wed, 3 Jul 2024 10:45:09 +0200 Subject: [PATCH] changes after review --- q2_amr/amrfinderplus/database.py | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/q2_amr/amrfinderplus/database.py b/q2_amr/amrfinderplus/database.py index 878fb58..ec1e686 100644 --- a/q2_amr/amrfinderplus/database.py +++ b/q2_amr/amrfinderplus/database.py @@ -28,14 +28,13 @@ def fetch_amrfinderplus_db() -> AMRFinderPlusDatabaseDirectoryFormat: def _copy_all(src_dir, des_dir): # Copies all files from source directory to destination directory for file in os.listdir(src_dir): - src = os.path.join(src_dir, file) - des = os.path.join(des_dir, file) - duplicate(src, des) + duplicate(os.path.join(src_dir, file), os.path.join(des_dir, file)) def run_amrfinder_u(): + # The command "amrfinder -u" downloads the latest amrfinderplus database or + # updates it cmd = ["amrfinder", "-u"] - try: run_command(cmd, verbose=True) except subprocess.CalledProcessError as e: