def test_samtools_index_cmd():
"""samtools_index instantiates, runs and returns
correct form of cmd-line"""
obj = samtools_index.Samtools_Index("samtools")
target = ' '.join(["samtools", "index", BAM_FILE])
stats = obj.run(BAM_FILE)
assert_equal(stats.command, target)
def test_samtools_index_exec():
"""Run samtools_index on test data and compare output
to precomputed target"""
obj = samtools_index.Samtools_Index("samtools")
result = obj.run(BAM_FILE)
# test to see if it has produced the bai file.
if not os.path.isfile(result.bai):
return False
def test_samtools_index_notexec():
"""Error thrown if samtools_index exe not executable"""
try:
obj = samtools_index.Samtools_Index("LICENSE")
except NotExecutableError:
return True
else:
return False
def test_samtools_index_exec_notexist():
"""Error thrown if samtools_index executable does not exist"""
try:
obj = samtools_index.Samtools_Index(os.path.join(".", "samtools"))
except NotExecutableError:
return True
else:
return False
def test_samtools_index():
"""Samtools_index instantiates with cmd-line if Samtools_index
is in $PATH"""
samtools_index.Samtools_Index("samtools")
