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#467 potential fatovcf version print out #475

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merged 1 commit into from
Jul 14, 2022
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#467 potential fatovcf version print out #475

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7 changes: 7 additions & 0 deletions pangolin/utils/initialising.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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:
Expand Down Expand Up @@ -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)

Expand Down