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#!/usr/bin/env python
"""Tests for availability of pyani dependencies
We only test for dependencies from non-standard libraries.
These tests are intended to be run using the nose package
(see https://nose.readthedocs.org/en/latest/).
"""
import subprocess
import sys
from nose.tools import assert_equal, nottest
def test_import_biopython():
"""Test Biopython import."""
import Bio
def test_import_matplotlib():
"""Test matplotlib import."""
import matplotlib
def test_import_numpy():
"""Test numpy import."""
import numpy
def test_import_pandas():
"""Test pandas import."""
import pandas
def test_import_scipy():
"""Test scipy import."""
import scipy
def test_run_blast():
"""Test that BLAST+ is runnable."""
cmd = "blastn -version"
result = subprocess.run(
cmd,
shell=sys.platform != "win32",
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
check=True,
)
print(result.stdout)
assert_equal(result.stdout[:6], b"blastn")
@nottest
def test_run_blastall():
"""Test that legacy BLAST is runnable."""
cmd = "blastall"
# Can't use check=True, as blastall without arguments returns 1!
result = subprocess.run(
cmd,
shell=sys.platform != "win32",
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
)
print(result.stdout)
assert_equal(result.stdout[1:9], b"blastall")
def test_run_nucmer():
"""Test that NUCmer is runnable."""
cmd = "nucmer --version"
result = subprocess.run(
cmd,
shell=sys.platform != "win32",
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
check=True,
)
print(result.stderr) # NUCmer puts output to STDERR!
assert_equal(result.stderr[:6], b"nucmer")
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