def test_samtools_idxstats_notexec():
"""Error thrown if samtools_idxstats exe not executable"""
try:
obj = samtools_idxstats.Samtools_Idxstats("LICENSE")
except NotExecutableError:
return True
else:
return False
def test_samtools_idxstats_exec():
"""Run samtools_idxstats on test data and compare output
to precomputed target"""
obj = samtools_idxstats.Samtools_Idxstats("samtools")
result = obj.run(BAM_FILE, OUTFILE)
with open(TARGET, "r") as target_fh:
with open(result.cov, "r") as test_fh:
assert_equal(target_fh.read(), test_fh.read())
def test_samtools_idxstats_exec_notexist():
"""Error thrown if samtools_idxstats executable does not exist"""
try:
obj = samtools_idxstats.Samtools_Idxstats(os.path.join(
".", "samtools"))
except NotExecutableError:
return True
else:
return False
def test_samtools_idxstats_cmd():
"""samtools_idxstats instantiates, runs and returns
correct form of cmd-line"""
# checking and making the output folder is staying in for now
if not os.path.exists(OUTDIR):
os.makedirs(OUTDIR)
obj = samtools_idxstats.Samtools_Idxstats("samtools")
target = ' '.join([
"samtools", "idxstats", BAM_FILE, "|", "grep", '-v', "'*'", "|",
"sort", "--reverse", "-n", "-k3", ">", OUTFILE
])
stats = obj.run(BAM_FILE, OUTFILE)
assert_equal(stats.command, target)
def test_samtools_idxstats():
"""Samtools_Idxstats instantiates with cmd-line if Samtools_Idxstats
is in $PATH"""
samtools_idxstats.Samtools_Idxstats("samtools")
