def test_ls(datadir_mgr):
"""Test ls command. """
test_file_paths = []
test_file_paths += datadir_mgr.paths_from_scope(module="1prefixing_test")
test_file_paths += datadir_mgr.paths_from_scope(module="2extraction_test")
test_file_paths += datadir_mgr.paths_from_scope(module="3indexing_test")
datadir_mgr.add_scope("prefix", module="1prefixing_test")
datadir_mgr.add_scope("extract", module="2extraction_test")
datadir_mgr.add_scope("index", module="3indexing_test")
with datadir_mgr.in_tmp_dir(
inpathlist=test_file_paths,
save_outputs=True,
excludepatterns=["*.log"],
):
output = sh.bionorm(["ls", "--recurse", ORGANISM_DIR])
lines_out = output.count("\n")
assert lines_out == len(test_file_paths)
assert not sh.bionorm(["ls", "-r", "--invalid", ORGANISM_DIR]).count(
"\n") # no invalid filename
assert not sh.bionorm(["ls", "-r", "--unrecognized", ORGANISM_DIR
]).count("\n") # no unrecognized filenames
UNREC_PATH.touch()
assert 1 == sh.bionorm(["ls", "-ru", ORGANISM_DIR
]).count("\n") # now 1 unrecognized filename
UNREC_PATH.unlink()
for badname, reason in ANN_INVALID_LIST:
badpath = ANN_PATH / badname
badpath.touch()
print(f"testing {reason}")
jsondict = sh.bionorm(["ls", "-rji", ORGANISM_DIR])
result_dict = json.loads(str(jsondict))
assert "invalid_key" in result_dict
assert result_dict["invalid_key"] == reason
badpath.unlink()
def test_install_gffread(datadir_mgr):
"""Test install gffread."""
with datadir_mgr.in_tmp_dir():
output = sh.bionorm([
"install",
"gffread",
])
print(output)
def test_install_genometools(datadir_mgr):
"""Test install genometools"""
with datadir_mgr.in_tmp_dir():
print("installing gffread")
output = sh.bionorm([
"install",
"genometools",
])
print(output)
def test_install_samtools(datadir_mgr):
"""Test install samtools"""
with datadir_mgr.in_tmp_dir():
print("installing samtools")
output = sh.bionorm([
"install",
"samtools",
])
print(output)
def test_version(tmp_path):
print("testing version")
with working_directory(tmp_path):
try:
output = sh.bionorm(["--version"])
except sh.ErrorReturnCode as e:
print(e)
pytest.fail(e)
print(output)
assert "version" in output
def test_index_gff(datadir_mgr):
"""Test index_gff."""
datadir_mgr.add_scope("prefix", module="1prefixing_test")
with datadir_mgr.in_tmp_dir(
inpathlist=[GFF_PATH],
save_outputs=True,
excludepatterns=["*.log"],
):
output = sh.bionorm(["index-gff", str(GFF_PATH)])
print(output)
def test_cli(tmp_path):
print("testing basic cli function")
with working_directory(tmp_path):
try:
output = sh.bionorm()
except sh.ErrorReturnCode as e:
print(e)
pytest.fail(e)
print(output)
assert "Usage:" in output
assert "Options:" in output
assert "Commands:" in output
def test_extraction(datadir_mgr):
"""Test command extract-fasta."""
datadir_mgr.add_scope("prefix", module="1prefixing_test")
with datadir_mgr.in_tmp_dir(inpathlist=PREFIXING_LIST,
save_outputs=True,
excludepatterns=["*.log"]):
output = sh.bionorm(["extract-fasta", str(GFF_PATH), str(FASTA_PATH)])
print(output)
loglist = [fp.name for fp in (Path.cwd() / "logs").glob("*")]
assert len(loglist) is 1
assert "bionorm-extract-fasta_0.log" in loglist
outfilelist = [fp.name for fp in ANN_PATH.glob("*")]
expectedlist = [p.name for p in EXTRACTION_LIST]
for filename in expectedlist:
assert filename in outfilelist
assert fasta_count(PROTEIN_PATH) == PROTEIN_COUNT
assert fasta_count(CDS_PATH) == PROTEIN_COUNT
def test_consistency(datadir_mgr):
"""Test consistency"""
datadir_mgr.add_scope("prefix", module="1prefixing_test")
datadir_mgr.add_scope("extract", module="2extraction_test")
with datadir_mgr.in_tmp_dir(
inpathlist=[
CDS_PATH,
GFF_PATH,
FASTA_PATH,
MRNA_PATH,
TRANSCRIPT_PATH,
],
save_outputs=True,
excludepatterns=["*.log"],
):
output = sh.bionorm(["consistency", "--help"])
print(output)
def test_prefix_fasta(datadir_mgr):
"""Test command prefix-fasta."""
datadir_mgr.download(
download_url=DOWNLOAD_URL,
files=[RAW_FASTA_FILE],
scope="function",
md5_check=True,
gunzip=True,
progressbar=False,
)
with datadir_mgr.in_tmp_dir(
inpathlist=[RAW_FASTA_FILE],
save_outputs=True,
excludepatterns=["*.log"],
):
try:
output = sh.bionorm([
"prefix-fasta",
"--genver",
"5",
"--genus",
"medicago",
"--species",
"truncatula",
"--infra_id",
"jemalong_A17",
"--key",
"FAKE",
RAW_FASTA_FILE,
])
except sh.ErrorReturnCode as e:
print(e)
pytest.fail(e)
print(output)
loglist = list((Path.cwd() / "logs").glob("*"))
assert len(loglist) is 1
assert str(loglist[0].name) == "bionorm-prefix-fasta_0.log"
outdir_path = Path(GENOME_PATH.parts[0])
subdirname = list(outdir_path.glob("*"))[0].parts[-1]
assert subdirname == GENOME_PATH.parts[1]
subdir_path = outdir_path / subdirname
outfilename = list(subdir_path.glob("*"))[0].name
assert outfilename == FASTA_PATH.parts[2]
assert fasta_count(Path(RAW_FASTA_FILE)) == fasta_count(FASTA_PATH)
