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test_requirements.py
Kurtz, Prof. Dr. Stefan authored
differences to Phybema as described in the B.Sc.-thesis of Birgitta P"auker:
1) use a python implementation of neighor joining. This saves
system call since the neighbor-joining algorithm is called
as a python function
2) conversion of output format is not necessary anymore. For
all distance estimators we require that they output a matrix in
phylip-format, either as a triangle or full matrix and with or
without zero-values on the main diagonal Code owners
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test_requirements.py 1.68 KiB
#!/usr/bin/env python3
'''
Script to test if needed programs can be found in the path.
author: Birgitta Päuker
'''
import shutil, sys, subprocess, re
# Function to test if needed programs can be found in the path.
def check_req():
# Test if mash (version >=2.1) is in the path
if not shutil.which('mash'):
sys.stderr.write("{}: mash is not in your path.\n".format(sys.argv[0]))
exit(1)
else:
try:
output = subprocess.run(["mash", "--version"],stdout=subprocess.PIPE,
stderr=subprocess.PIPE, universal_newlines=True)
except:
sys.stderr.write("{}:Checking mash version failed\n".format(sys.argv[0]))
exit(1)
if float(output.stdout) < 2.1:
sys.stderr.write("{}: mash version >= 2.1 needed.\n".format(sys.argv[0]))
exit(1)
# Test if ete3 is in the path
if not shutil.which('ete3'):
sys.stderr.write("{}: ete3 is not in your path.\n".format(sys.argv[0]))
exit(1)
# Test if python (version >=3.5) is in the path
if not shutil.which('python3'):
sys.stderr.write("{}: python3 is not in your path.\n".format(sys.argv[0]))
exit(1)
else:
try:
output = subprocess.run(["python3", "--version"],stdout=subprocess.PIPE,
stderr=subprocess.PIPE, universal_newlines=True)
except:
sys.stderr.write("{}: Checking python3 version failed\n"
.format(sys.argv[0]))
exit(1)
version = list(filter(None, (re.split(r'\s',output.stdout))))[-1]
versionnum = ".".join(version.split(".")[:2])
if float(versionnum) < 3.5:
sys.stderr.write("{}: python3 version >= 3.5 needed.\n"
.format(sys.argv[0]))
exit(1)