def main():
args = handle_program_options()
try:
# Load biom format file
biomf = biom.load_table(args.input_biom_fp)
except TypeError as te:
sys.exit(
"The data in the path does not appear to be a BIOM format table. "
"Error: {}.".format(te))
# Determine OTUIDs present in each sample
sample_otus = oc.assign_otu_membership(biomf)
try:
# Parse mapping file
header, imap = util.parse_map_file(args.mapping_file)
except ValueError as ve:
sys.exit("Error: {}.".format(ve))
# Get relevant category information
group_data = util.gather_categories(imap, header, [args.category_column])
# Initialize results dict in group_data with {"otuids": set()} for each category
for group in group_data:
group_data[group].results["otuids"] = set()
# Collect all OTUIDs present in each category
for sid in sample_otus:
group = sample_group(sid, group_data)
group_data[group].results["otuids"].update(sample_otus[sid])
if args.reverse:
# Get shared OTUIDs
shared = shared_otuids(group_data)
# Write out shared OTUIDs results
shared_df = pd.DataFrame.from_dict(shared, orient="index").T
shared_df.to_csv(args.reverse, sep="\t", index=False)
# Create input for unique_otus
group_otuids = {
group: group_data[group].results["otuids"]
for group in group_data
}
# Write out unique OTUIDs to file
write_uniques(args.output_dir, args.prefix, unique_otuids(group_otuids))
def test_fuzzy_lookup(self):
"""
Testing fuzzy_lookup() function of otu_calc.py.
:return: Returns OK if the test goals were achieved, otherwise
raises error.
"""
self.result1 = oc.assign_otu_membership(self.biom)['Sample2']
self.result = oc.fuzzy_lookup(self.result1, ['Escherichia_spp.'])
# Obtaining manual result to be compared against.
hand_calc = 'Escherichia_spp.'
# Testing the validity of fuzzy_lookup() function.
self.assertIn(
hand_calc, str(self.result1),
msg='Error! Output is not a subset of input.'
)
def test_sdi(self):
"""
Testing sdi() function of otu_calc.py.
:return: Returns OK if the test goals were achieved, otherwise
raises error.
"""
self.result1 = oc.assign_otu_membership(self.biom)
fset = self.result1['Sample4']
self.result = oc.sdi(fset)
# Manual calculation of SDI
hand_calc = 0.636513937
# Testing the validity of sdi() function
self.assertAlmostEqual(
self.result, hand_calc, places=6,
msg='Error! SDI was calculated inacccurately.'
)
def test_print_membership(self):
"""
Testing print_membership() function of otu_calc.py. Output of this
function is written to a temporary file. The contents of the temporary
file are accessed and used to compare with expected output.
:return: Returns OK if the test goals were achieved, otherwise
raises error.
"""
self.result1 = oc.assign_otu_membership(self.biom)
# Writing the output of print_membership() to temporary file.
saveout = sys.stdout
temp_file2 = tempfile.NamedTemporaryFile(delete=False)
with open(temp_file2.name, 'w') as f:
sys.stdout = f
self.result = oc.print_membership(self.result1['Sample1'])
sys.stdout = saveout
# Obtaining the function output from output.txt file.
func_calc = []
with open(temp_file2.name, 'r') as out:
while True:
statement = out.readline()
func_calc.append(statement)
if not statement:
break
# Writing manual outputs to compare
hand_calc = [
'Halanaerobium_Halanaerobiumsaccharolyticum: 28.57%\n',
'Dolichospermum_spp.: 71.43%\n'
]
# Testing the validity of print_membership() function
self.assertListEqual(
func_calc[0:2], hand_calc,
msg='Error! Output does not print out the right information correctly.'
)
# Deleting temporary file.
os .unlink(temp_file2.name)
def test_assign_otu_membership(self):
"""
Testing assign_otu_membership() function of otu_calc.py.
:return: Returns OK if the test goals were achieved, otherwise
raises error.
"""
self.result = oc.assign_otu_membership(self.biom)
# Obtaining the values to be tested
result1 = bc.relative_abundance(self.biom, ['Sample1'])
hand_calc = result1.values()[0].values()
func_calc = [0.714286, 0.285714]
# Testing the validity of assign_otu_membership() function
for hand, func in zip(hand_calc, func_calc):
self.assertAlmostEqual(
hand, func, places=5,
msg='Error! OTU membership calculations are inaccurate!'
)
def main():
args = handle_program_options()
try:
# Load biom format file
biomf = biom.load_table(args.input_biom_fp)
except TypeError as te:
sys.exit("The data in the path does not appear to be a BIOM format table. "
"Error: {}.".format(te))
# Determine OTUIDs present in each sample
sample_otus = oc.assign_otu_membership(biomf)
try:
# Parse mapping file
header, imap = util.parse_map_file(args.mapping_file)
except ValueError as ve:
sys.exit("Error: {}.".format(ve))
# Get relevant category information
group_data = util.gather_categories(imap, header, [args.category_column])
# Initialize results dict in group_data with {"otuids": set()} for each category
for group in group_data:
group_data[group].results["otuids"] = set()
# Collect all OTUIDs present in each category
for sid in sample_otus:
group = sample_group(sid, group_data)
group_data[group].results["otuids"].update(sample_otus[sid])
if args.reverse:
# Get shared OTUIDs
shared = shared_otuids(group_data)
# Write out shared OTUIDs results
shared_df = pd.DataFrame.from_dict(shared, orient="index").T
shared_df.to_csv(args.reverse, sep="\t", index=False)
# Create input for unique_otus
group_otuids = {group: group_data[group].results["otuids"] for group in group_data}
# Write out unique OTUIDs to file
write_uniques(args.output_dir, args.prefix, unique_otuids(group_otuids))
def test_assign_otu_membership(self):
"""
Testing assign_otu_membership() function of otu_calc.py.
:return: Returns OK if the test goals were achieved, otherwise
raises error.
"""
self.biomf = biom.load_table("phylotoast/test/test.biom")
self.result = oc.assign_otu_membership(self.biomf)
# Obtaining the values to be tested
hand_calc = {"S9": ["GG_OTU_2", "GG_OTU_3", "GG_OTU_5"],
"S3": ["GG_OTU_1", "GG_OTU_2", "GG_OTU_4", "GG_OTU_5"],
"S6": ["GG_OTU_1", "GG_OTU_2", "GG_OTU_3", "GG_OTU_4", "GG_OTU_5"]}
# Testing the validity of assign_otu_membership() function
for sid in ["S3", "S6", "S9"]:
self.assertListEqual(
sorted(hand_calc[sid]), sorted(self.result[sid]),
msg="Error! OTU membership calculations are inaccurate!"
)
def test_assign_otu_membership(self):
"""
Testing assign_otu_membership() function of otu_calc.py.
:return: Returns OK if the test goals were achieved, otherwise
raises error.
"""
self.biomf = biom.load_table("phylotoast/test/test.biom")
self.result = oc.assign_otu_membership(self.biomf)
# Obtaining the values to be tested
hand_calc = {
"S9": ["GG_OTU_2", "GG_OTU_3", "GG_OTU_5"],
"S3": ["GG_OTU_1", "GG_OTU_2", "GG_OTU_4", "GG_OTU_5"],
"S6": ["GG_OTU_1", "GG_OTU_2", "GG_OTU_3", "GG_OTU_4", "GG_OTU_5"]
}
# Testing the validity of assign_otu_membership() function
for sid in ["S3", "S6", "S9"]:
self.assertListEqual(
sorted(hand_calc[sid]),
sorted(self.result[sid]),
msg="Error! OTU membership calculations are inaccurate!")