def legacy_tetra_mpl_namespace(tmp_path, legacy_ani_namespace):
"""Namespace for legacy ANIm script tests.
Uses the base namespace to run ANIm with mpl output
"""
return modify_namespace(legacy_ani_namespace,
method="TETRA",
gmethod="mpl")
def legacy_anim_mpl_namespace(tmp_path, legacy_ani_namespace):
"""Namespace for legacy ANIm script tests.
Runs ANIm with matplotlib output
"""
return modify_namespace(legacy_ani_namespace, gmethod="mpl")
def legacy_anib_sns_namespace(tmp_path, legacy_ani_namespace):
"""Namespace for legacy ANIm script tests.
Uses the base namespace to run ANIm with seaborn output
"""
return modify_namespace(legacy_ani_namespace, method="ANIb")
def kraken_namespace(base_download_namespace, tmp_path):
"""Namespace for downloading C. blochmannia with Kraken labels."""
return modify_namespace(base_download_namespace,
kraken=True,
outdir=tmp_path / "kraken")
def dryrun_namespace(base_download_namespace):
"""Namespace for pyani download dry run."""
return modify_namespace(base_download_namespace, dryrun=True)
def setUp(self):
"""Configure parameters for tests."""
testdir = Path("tests")
self.testdirs = TestDirs(
testdir / "test_output" / "legacy_scripts",
testdir / "test_targets" / "legacy_scripts",
testdir / "test_output" / "legacy_scripts" / "C_blochmannia",
)
self.testdirs.outdir.mkdir(exist_ok=True)
self.exes = Executables("nucmer", "delta-filter", "blastn", "blastall",
"makeblastdb", "formatdb")
# Base namespaces for each script
self.base_download = Namespace(
outdirname=self.testdirs.dldir,
taxon="203804",
verbose=False,
force=True,
noclobber=False,
logfile=None,
format="fasta",
email="*****@*****.**",
retries=20,
batchsize=10000,
timeout=10,
)
self.base_ani = Namespace(
outdirname=self.testdirs.outdir /
f"ANIm_seaborn_{anim.get_version()}",
indirname=self.testdirs.dldir,
verbose=False,
force=True,
fragsize=1020,
logfile="test_ANIm.log",
skip_nucmer=False,
skip_blastn=False,
noclobber=False,
nocompress=False,
graphics=True,
gformat="pdf,png",
gmethod="seaborn",
labels=None,
classes=None,
method="ANIm",
scheduler="multiprocessing",
workers=None,
sgeargs=None,
sgegroupsize=10000,
maxmatch=False,
nucmer_exe=self.exes.nucmer,
filter_exe=self.exes.filter,
blastn_exe=self.exes.blastn,
blastall_exe=self.exes.blastall,
makeblastdb_exe=self.exes.makeblastdb,
formatdb_exe=self.exes.formatdb,
write_excel=False,
rerender=False,
subsample=None,
seed=None,
jobprefix="ANI",
)
# Null logger instance
self.logger = logging.getLogger("TestLegacyScripts logger")
self.logger.addHandler(logging.NullHandler())
# Command-line namespaces
self.argsdict = {
"download":
self.base_download,
"anim_seaborn":
self.base_ani, # Baseline namespace
"anim_mpl":
modify_namespace(
self.base_ani,
{
"outdirname":
self.testdirs.outdir / f"ANIm_mpl_{anim.get_version()}",
"gmethod": "mpl",
},
),
"anib_seaborn":
modify_namespace(
self.base_ani,
{
"outdirname": self.testdirs.outdir / "ANIb_seaborn",
"method": "ANIb"
},
),
"anib_mpl":
modify_namespace(
self.base_ani,
{
"outdirname": self.testdirs.outdir / "ANIb_mpl",
"gmethod": "mpl",
"method": "ANIb",
},
),
"tetra_seaborn":
modify_namespace(
self.base_ani,
{
"outdirname": self.testdirs.outdir / "TETRA_seaborn",
"method": "TETRA",
},
),
"tetra_mpl":
modify_namespace(
self.base_ani,
{
"outdirname": self.testdirs.outdir / "TETRA_mpl",
"gmethod": "mpl",
"method": "TETRA",
},
),
}