def test_bowtie2_build_exec_notexist():
"""Error thrown if bowtie_build executable does not exist"""
try:
obj = bowtie_build.Bowtie2_Build(os.path.join(".", "bowtie2-build"))
except NotExecutableError:
return True
else:
return False
def test_bowtie2_build_notexec():
"""Error thrown if bowtie2-build not executable"""
try:
obj = bowtie_build.Bowtie2_Build("LICENSE")
except NotExecutableError:
return True
else:
return False
def test_bowtie_index_exec():
"""Run bowtie_index on test FQ data and compare output
to precomputed target"""
obj = bowtie_build.Bowtie2_Build("bowtie2-build")
result = obj.run(DATABASE, FA_INDEX)
# test to see if it has produced the bai file.
if not os.path.isfile(result.index + "1"):
return False
def test_bowtie2_build_cmd():
"""bowtie2-build returns correct form of cmd-line"""
bowtie2_idx = bowtie_build.Bowtie2_Build("bowtie2-build")
target = ' '.join(["bowtie2-build",
"--quiet",
"-f",
DATABASE,
FA_INDEX])
result = bowtie2_idx.run(DATABASE, FA_INDEX, dry_run=True)
assert_equal(result.command, target)
def test_bowtie_index_cmd():
"""bowtie2 instantiates, runs and returns correct form of cmd-line"""
obj = bowtie_build.Bowtie2_Build("bowtie2-build")
target = ' '.join(["bowtie2-build",
"--quiet",
"-f",
DATABASE,
FA_INDEX])
assert_equal(obj.run(DATABASE, FA_INDEX, dry_run=True),
target)
def test_bowtie2_build_exec():
"""bowtie2-build indexes the file correctly"""
bowtie2_idx = bowtie_build.Bowtie2_Build("bowtie2-build")
result = bowtie2_idx.run(DATABASE, FA_INDEX)
# Test for equality of output and target MD5 hashes
for fname in os.listdir(OUTDIR):
with open(os.path.join(OUTDIR, fname), "rb") as outfh:
outhash = hashlib.md5()
outhash.update(outfh.read())
with open(os.path.join(TARGETDIR, fname), "rb") as tgtfh:
tgthash = hashlib.md5()
tgthash.update(tgtfh.read())
assert_equal(tgthash.digest(), outhash.digest())
def test_bowtie2_build_path():
"""bowtie2-build executable is in $PATH"""
bowtie_build.Bowtie2_Build("bowtie2-build")
def test_bowtie():
"""bowtie_index instantiates with cmd-line if bowtie is in $PATH"""
bowtie_build.Bowtie2_Build("bowtie2-build")