def test_predict(version, clss, exp_val):
""" Pretty much a repeat of test_rcds. """
with open(model_filepath(version), "rb") as handle:
model = Model.read(handle)
required_cols = list(model.hmm_lengths.keys())
files = test_files(version)
with open(files["hmmer_text"], "r") as handle:
parsed = HMMER.from_file(
handle,
model.hmm_lengths,
"hmmer3-text",
)
counts = cazy_counts_multi([parsed], ["test"], required_cols)
pred = model.predict(counts)
rcds = pred.rcd
rcds_dict = dict()
for res in rcds:
assert res.label == "test"
rcds_dict[(res.label, res.nomenclature,
res.nomenclature_class)] = res.value
# Checks that results are accurate to 5 decimal places.
assert_almost_equal(
exp_val,
rcds_dict[("test", "nomenclature3", clss)],
decimal=5
)
return
def test_parse_hmmer_text_output(version, idx, col, exp_val):
with open(model_filepath(version), "rb") as handle:
model = Model.read(handle)
files = test_files(version)
with open(files["hmmer_text"], "r") as handle:
sample = list(
HMMER.from_file(
handle,
model.hmm_lengths,
"hmmer3-text",
))
assert getattr(sample[idx], col) == exp_val
return
def test_cazy_counts(version, hmm, exp_val):
with open(model_filepath(version), "rb") as handle:
model = Model.read(handle)
required_cols = list(model.hmm_lengths.keys())
files = test_files(version)
with open(files["hmmer_text"], "r") as handle:
parsed = HMMER.from_file(
handle,
model.hmm_lengths,
"hmmer3-text",
)
counts = cazy_counts(parsed, required_cols)
column_index = required_cols.index(hmm)
assert counts[column_index] == exp_val
return
def test_pca(version, pc, exp_val):
with open(model_filepath(version), "rb") as handle:
model = Model.read(handle)
required_cols = list(model.hmm_lengths.keys())
files = test_files(version)
with open(files["hmmer_text"], "r") as handle:
parsed = HMMER.from_file(
handle,
model.hmm_lengths,
"hmmer3-text",
)
counts = cazy_counts_multi([parsed], ["test"], required_cols)
pred = model.predict(counts)
trans = pred.pca
# Checks that results are accurate to 5 decimal places.
column_index = trans.columns.index(pc)
assert_almost_equal(exp_val, trans.arr[0, column_index], decimal=5)
return
def main(): # noqa
""" The cli interface to CATAStrophy. """
try:
args = cli(prog=sys.argv[0], args=sys.argv[1:])
except MyArgumentError as e:
print(e.message, file=sys.stderr)
sys.exit(e.errno)
infile_names = [f.name for f in args.infile]
if args.labels is None:
labels = infile_names
elif len(args.labels) != len(args.infile):
msg = ("argument labels and inhandles: \n"
"When specified, the number of labels must be the same as the "
"number of input files. Exiting.\n")
print(msg, file=sys.stderr)
sys.exit(EXIT_CLI)
else:
labels = args.labels
if args.model_file is not None:
model = Model.read(args.model_file)
else:
with open(data.model_filepath(args.model_version), "rb") as handle:
model = Model.read(handle)
try:
runner(
args.infile,
args.outhandle,
args.pca_handle,
args.counts_filepath,
labels,
args.file_format,
model,
)
except ParseError as e:
if e.line is not None:
header = "Failed to parse file <{}> at line {}.\n".format(
e.filename, e.line)
else:
header = "Failed to parse file <{}>.\n".format(e.filename)
print("{}\n{}".format(header, e.message), file=sys.stderr)
sys.exit(EXIT_INPUT_FORMAT)
except HMMError as e:
msg = ("Encountered an hmm that wasn't present in the training data.\n"
f"Offending HMMs were: {', '.join(e.hmms)}")
print(msg, file=sys.stderr)
sys.exit(EXIT_INPUT_FORMAT)
pass
except OSError as e:
msg = (
"Encountered a system error.\n"
"We can't control these, and they're usually related to your OS.\n"
"Try running again.\n")
print(msg, file=sys.stderr)
print(e.strerror, file=sys.stderr)
sys.exit(EXIT_SYSERR)
except MemoryError:
msg = ("Ran out of memory!\n"
"Catastrophy shouldn't use much RAM, so check other "
"processes and try running again.")
print(msg, file=sys.stderr)
sys.exit(EXIT_SYSERR)
except KeyboardInterrupt:
print("Received keyboard interrupt. Exiting.", file=sys.stderr)
sys.exit(EXIT_KEYBOARD)
except Exception as e:
msg = (
"I'm so sorry, but we've encountered an unexpected error.\n"
"This shouldn't happen, so please file a bug report with the "
"authors.\nWe will be extremely grateful!\n\n"
"You can email us at {}.\n"
"Alternatively, you can file the issue directly on the repo "
"<https://bitbucket.org/ccdm-curtin/catastrophy/issues>\n\n"
"Please attach a copy of the following message:").format(__email__)
print(e, file=sys.stderr)
traceback.print_exc(file=sys.stderr)
sys.exit(EXIT_UNKNOWN)
return