From bfbf3b9a8b65844d55c1eda8608cdb8a7fef25dd Mon Sep 17 00:00:00 2001 From: aineniamh Date: Thu, 30 Jun 2022 22:17:36 +0100 Subject: [PATCH] #467 potential fatovcf version print out --- pangolin/utils/initialising.py | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/pangolin/utils/initialising.py b/pangolin/utils/initialising.py index 6deae29..4a51e60 100644 --- a/pangolin/utils/initialising.py +++ b/pangolin/utils/initialising.py @@ -205,6 +205,12 @@ def get_version(programs): version = output.stdout.strip().split()[-1].strip('()v') print(f"{program.split()[0]} {version}") +def print_faToVf_version(): + output = subprocess.run("faToVcf -verbose=2 -h 2>&1 | grep '#'", shell=True, check=True, + stdout=subprocess.PIPE, encoding='utf-8') + version = output.stdout.split(' ')[-2] + print(f"faToVcf: {version}") + def print_conda_version(pkg_list): for pkg in pkg_list: try: @@ -233,6 +239,7 @@ def print_versions_exit(config): print(f"pangolin-assignment: {config[KEY_PANGOLIN_ASSIGNMENT_VERSION]}") # Print versions of other important tools used by pangolin get_version(['usher', 'gofasta', 'minimap2']) + print_faToVf_version() # print_conda_version(['usher', 'ucsc-fatovcf', 'gofasta', 'minimap2']) sys.exit(0)