def test_flash_notexec():
"""Error thrown if flash exe not executable"""
try:
obj = flash.Flash("LICENSE")
except NotExecutableError:
return True
else:
return False
def test_flash_exec_notexist():
"""Error thrown if flash executable does not exist"""
try:
obj = flash.Flash(os.path.join(".", "flash"))
except NotExecutableError:
return True
else:
return False
def test_flash_cmd():
"""flash instantiates, runs and returns correct form of cmd-line"""
obj = flash.Flash("flash")
target = ' '.join(["flash", "--max-overlap", "250",
"--threads", "4", "-o", os.path.join(OUTDIR, PREFIX),
READS1, READS2])
assert_equal(obj.run(READS1, READS2, 4, OUTDIR, PREFIX, dry_run=True),
target)
def test_flash_exec():
"""Run flash on test data and compare output to precomputed target
this often does not produce the same result twice. So we may have
to disable this test"""
obj = flash.Flash("flash")
result = obj.run(READS1, READS2, 4, OUTDIR, PREFIX, dry_run=False)
# call function to sort the data. returned as a sorted(set)
# the flash output is not sorted, so a direct comparason of the file
# does not work. So have to sort first.
targed_data_sorted = sort_flash_output(TARGET)
# outfileextended - name from named tuple and originally
# from build_command
test_data_sorted = sort_flash_output(result.outfileextended)
assert_equal(targed_data_sorted, test_data_sorted)
def test_flash():
"""flash instantiates with cmd-line if flash is in $PATH"""
assemble = flash.Flash("flash")