def test_all_use_counts():
"""
Tests that BUSCO runs using arguments provided as a string.
"""
base_dir = os.path.join(os.path.dirname(__file__), '..', 'aux_data')
sample_dir = os.path.join(base_dir, test_reference, "samples_METs_small")
salmon_dir = os.path.join(base_dir, test_reference, "samples_METs",
"salmon_quant")
output_dir = os.path.join(base_dir, "test_out_V")
reference_dir = os.path.join(base_dir, test_reference, "sample_ref")
os.system("rm -rf " + output_dir)
string_arguments = " ".join([
"all", "--database", "mmetsp", "--sample_dir", sample_dir,
"--mets_or_mags", "mets", "--out_dir", output_dir, "--busco_threshold",
str(30), "--individual_or_summary", "individual", '--organisms',
'Chromera', "--filter_metric", "pid", '--taxonomy_organisms', 'genus',
"--ref_fasta", "reference.pep.fa", "--reference_dir", reference_dir,
"--use_salmon_counts", "--salmon_dir", salmon_dir
])
eukulele(string_arguments=string_arguments)
samplenames = [curr.split(".")[0] for curr in os.listdir(sample_dir)]
busco_out = os.path.join(output_dir, "busco_assessment", samplenames[0],
"individual",
"summary_" + samplenames[0] + ".tsv")
assert os.path.isfile(busco_out)
def test_individual():
'''
Test running the BUSCO functionality with individually specified
arguments, rather than a full class/other functional group.
'''
base_dir = os.path.join(os.path.dirname(__file__), '..', 'aux_data')
sample_dir = os.path.join(base_dir, test_reference, "samples_MAGs")
output_dir = os.path.join(base_dir, "test_out_E")
os.system("rm -rf " + output_dir)
reference_dir = os.path.join(base_dir, test_reference, "sample_ref_MAG")
string_arguments = " ".join([
"all", "--database", "mmetsp", "--sample_dir", sample_dir,
"--mets_or_mags", "mags", "--out_dir", output_dir, "-i", '--organisms',
'Chromera', '--taxonomy_organisms', 'genus', "--reference_dir",
reference_dir
])
eukulele(string_arguments=string_arguments)
samplenames = [curr.split(".")[0] for curr in os.listdir(sample_dir)]
busco_out = os.path.join(output_dir, "busco_assessment", samplenames[0],
"individual",
"summary_" + samplenames[0] + ".tsv")
assert os.path.isfile(busco_out)
def test_all_commandline():
"""
Tests that alignment works properly using a string of arguments.
"""
base_dir = os.path.join(os.path.dirname(__file__), '..', 'aux_data')
sample_dir = os.path.join(base_dir, test_reference, "samples_METs_small")
output_dir = os.path.join(base_dir, "test_out_R")
reference_dir = os.path.join(base_dir, test_reference, "sample_ref")
#EUKulele alignment --database mmetsp --sample_dir
# tests/aux_data/mmetsp/samples_METs_small --mets_or_mags mets
# --out_dir tests/test_out --organisms Chromera --taxonomy_organisms
# genus --reference_dir tests/aux_data/mmetsp
string_arguments = " ".join([
"alignment", "--database", "mmetsp", "--sample_dir", sample_dir,
"--mets_or_mags", "mets", "--out_dir", output_dir, "--organisms",
"Chromera", "--ref_fasta", "reference.pep.fa", "--taxonomy_organisms",
"genus", "--reference_dir", reference_dir
])
eukulele(string_arguments=string_arguments)
samplenames = [curr.split(".")[0] for curr in os.listdir(sample_dir)]
est_out = os.path.join(output_dir, "taxonomy_estimation",
samplenames[0] + "-estimated-taxonomy.out")
assert os.path.isfile(est_out)
def test_busco_file():
'''
Tests the functionality of using a file to specify the organisms
to explore via BUSCO.
'''
base_dir = os.path.join(os.path.dirname(__file__), '..', 'aux_data')
sample_dir = os.path.join(base_dir, test_reference, "samples_MAGs")
output_dir = os.path.join(base_dir, "test_out_K")
os.system("rm -rf " + output_dir)
reference_dir = os.path.join(base_dir, test_reference, "sample_ref_MAG")
string_arguments = " ".join([
"--database", "mmetsp", "--sample_dir", sample_dir, "--mets_or_mags",
"mags", "--out_dir", output_dir, "-i", '--busco_file',
os.path.join(base_dir, test_reference, "samples_MAGs",
"test_busco.tsv"), "--reference_dir", reference_dir
])
error = 0
eukulele(string_arguments=string_arguments)
samplenames = [curr.split(".")[0] for curr in os.listdir(sample_dir)]
busco_out = os.path.join(output_dir, "busco_assessment", samplenames[0],
"individual",
"summary_" + samplenames[0] + ".tsv")
out_prefix = samplenames[0]
assert os.path.isfile(busco_out)
def test_error_busco():
'''
Tests that we get an error when we use a BUSCO file that does
not exist.
'''
base_dir = os.path.join(os.path.dirname(__file__), '..', 'aux_data')
sample_dir = os.path.join(base_dir, test_reference, "samples_MAGs")
output_dir = os.path.join(base_dir, "test_out_K")
os.system("rm -rf " + output_dir)
reference_dir = os.path.join(base_dir, test_reference, "sample_ref")
string_arguments = " ".join([
"--database", "mmetsp", "--sample_dir", sample_dir, "--mets_or_mags",
"mags", "--out_dir", output_dir, "-i", '--busco_file',
os.path.join(base_dir, test_reference, "samples_MAGs",
"busco_file_fake.tsv"), "--reference_dir", reference_dir
])
error = 0
try:
eukulele(string_arguments=string_arguments)
except:
error = 1
assert error == 1
def test_tester():
base_dir = os.path.join(os.path.dirname(__file__), '..', 'aux_data')
sample_dir = os.path.join(base_dir, test_reference, "samples_MAGs")
output_dir = os.path.join(base_dir, "test_out")
reference_dir = os.path.join(base_dir, test_reference, "sample_ref")
os.system("rm -rf " + output_dir)
string_arguments = " ".join(["setup", "--test", "--database", "mmetsp", "--sample_dir", sample_dir,
"--mets_or_mags", "mags", "--out_dir", output_dir, "--ref_fasta",
"reference.pep.fa", "--reference_dir", reference_dir])
eukulele(string_arguments=string_arguments)
assert (not os.path.isdir(output_dir))
#def test_cleanup():
# base_dir = os.path.join(os.path.dirname(__file__), '..', 'aux_data')
# config_path = os.path.join(os.path.dirname(__file__), '..', 'aux_data', 'test_configs')
# base_configs = [os.path.join(config_path, 'curr_config_alignment.yaml'),\
# os.path.join(config_path, 'curr_config_setup.yaml')]
# successful_test = True
# for base_config in base_configs:
# with open(base_config) as f:
# config = yaml.load(f, Loader=yaml.FullLoader)
# config["reference"] = os.path.join(base_dir, test_reference)
# os.system("rm -rf " + os.path.join(config["output"]))
# successful_test = successful_test & (not os.path.isdir(os.path.join(config["output"])))
# successful_test = True
# assert successful_test
def test_all():
'''
Combined test case.
'''
base_dir = os.path.join(os.path.dirname(__file__), '..', 'aux_data')
base_config = os.path.join(os.path.dirname(__file__), '..', 'aux_data',
'config.yaml')
base_config_curr = os.path.join(os.path.dirname(__file__), '..',
'aux_data', 'config_O.yaml')
os.system("cp " + base_config + " " + base_config_curr)
with open(base_config_curr) as f:
config = yaml.load(f, Loader=yaml.FullLoader)
config["mets_or_mags"] = "mags"
config["reference"] = os.path.join(base_dir, test_reference,
"sample_ref_MAG")
config["samples"] = os.path.join(base_dir, "real-world-samples", "MAGs")
config["subroutine"] = "all"
config["individual_or_summary"] = "summary"
config["cutoff"] = os.path.join("tax-cutoffs.yaml")
config["output"] = os.path.join(base_dir, "test_out_all_K")
config["database"] = test_reference
config["organisms"] = ["Chromera"]
config["taxonomy_organisms"] = ["genus"]
config["download_reference"] = 0
config["column"] = "SOURCE_ID"
config["ref_fasta"] = "reference.pep.fa"
config["protein_map"] = "prot-map.json"
config["tax_table"] = "tax-table.txt"
config_path = os.path.join(base_dir, 'test_configs')
os.system("mkdir -p " + config_path)
config_file = os.path.join(config_path, 'curr_config_busco_O.yaml')
with open(config_file, 'w') as f:
yaml.dump(config, f)
eukulele(string_arguments=" ".join(["--config", config_file]))
samplenames = [
curr.split(".")[0] for curr in os.listdir(config["samples"])
]
busco_out = os.path.join(config["output"], "busco_assessment",
samplenames[0], "species_combined",
"summary_species_" + samplenames[0] + ".tsv")
out_prefix = samplenames[0]
mag_file = os.path.join(config["output"], "levels_mags",
out_prefix + '.' + "species")
assert (os.path.isfile(busco_out)) & (os.path.isfile(mag_file))
def test_busco():
base_dir = os.path.join(os.path.dirname(__file__), '..', 'aux_data')
base_config = os.path.join(os.path.dirname(__file__), '..', 'aux_data',
'config.yaml')
base_config_curr = os.path.join(os.path.dirname(__file__), '..',
'aux_data', 'config_all.yaml')
os.system("cp " + base_config + " " + base_config_curr)
with open(base_config_curr) as f:
config = yaml.load(f, Loader=yaml.FullLoader)
config["mets_or_mags"] = "mags"
config["reference"] = os.path.join(base_dir, test_reference, "sample_ref")
config["samples"] = os.path.join(base_dir, test_reference, "samples_MAGs")
config["cutoff"] = os.path.join("tax-cutoffs.yaml")
config["output"] = os.path.join(base_dir, "test_out_all")
config["database"] = test_reference
config["organisms"] = ["Chromera"]
config["taxonomy_organisms"] = ["genus"]
config["download_reference"] = 0
config["column"] = "SOURCE_ID"
config["ref_fasta"] = "reference.pep.fa"
config["protein_map"] = "prot-map.json"
config["tax_table"] = "tax-table.txt"
config_path = os.path.join(base_dir, 'test_configs')
os.system("mkdir -p " + config_path)
config_file = os.path.join(config_path, 'curr_config_busco_all.yaml')
config["subroutine"] = "alignment"
with open(config_file, 'w') as f:
yaml.dump(config, f)
eukulele(config=config_file)
config["subroutine"] = "busco"
with open(config_file, 'w') as f:
yaml.dump(config, f)
eukulele(config=config_file)
samplenames = [
curr.split(".")[0] for curr in os.listdir(config["samples"])
]
busco_out = os.path.join(config["output"], "busco_assessment",
samplenames[0], "individual",
"summary_" + samplenames[0] + ".tsv")
assert os.path.isfile(busco_out)
def test_error_busco_no_orgs():
base_dir = os.path.join(os.path.dirname(__file__), '..', 'aux_data')
sample_dir = os.path.join(base_dir, test_reference, "samples_MAGs")
output_dir = os.path.join(base_dir, "test_out_H")
os.system("rm -rf " + output_dir)
reference_dir = os.path.join(base_dir, test_reference, "sample_ref")
string_arguments = " ".join(["--database", "mmetsp", "--sample_dir", sample_dir,
"--mets_or_mags", "mags", "--out_dir", output_dir, "-i",
"--reference_dir", reference_dir])
error = 0
try:
eukulele(string_arguments=string_arguments)
except:
error = 1
assert error == 1
def test_setup_blast():
'''
Tests setup followed by a BLAST subroutine call.
'''
base_dir = os.path.join(os.path.dirname(__file__), '..', 'aux_data')
base_config = os.path.join(os.path.dirname(__file__), '..', 'aux_data',
'config.yaml')
base_config_curr = os.path.join(os.path.dirname(__file__), '..',
'aux_data', 'config_C.yaml')
os.system("cp " + base_config + " " + base_config_curr)
with open(base_config_curr) as f:
config = yaml.load(f, Loader=yaml.FullLoader)
config["mets_or_mags"] = "mags"
config["reference"] = os.path.join(base_dir, test_reference,
"sample_ref_MAG")
config["samples"] = os.path.join(base_dir, test_reference, "samples_MAGs")
config["subroutine"] = "setup"
config["alignment_choice"] = "blast"
config["cutoff"] = os.path.join("tax-cutoffs.yaml")
config["output"] = os.path.join(base_dir, "test_out_C")
config["database"] = test_reference
config["download_reference"] = 0
config["column"] = "SOURCE_ID"
config["ref_fasta"] = "reference.pep.fa"
config["protein_map"] = "prot-map.json"
config["tax_table"] = "tax-table.txt"
config_path = os.path.join(base_dir, 'test_configs')
os.system("mkdir -p " + config_path)
config_file = os.path.join(config_path, 'curr_config_alignment_C.yaml')
with open(config_file, 'w') as f:
yaml.dump(config, f)
eukulele(config=config_file)
assert os.path.isdir(os.path.join(config["reference"], "blast"))
config["subroutine"] = "alignment"
with open(config_file, 'w') as f:
yaml.dump(config, f)
eukulele(config=config_file)
outprefix = config["output"].split("/")[-1]
assert os.path.isfile(
os.path.join(config["output"], "taxonomy_counts",
outprefix + "_all_species_counts.csv"))
def test_setup_commandline():
base_dir = os.path.join(os.path.dirname(__file__), '..', 'aux_data')
sample_dir = os.path.join(base_dir, test_reference, "samples_METs_small")
output_dir = os.path.join(base_dir, "test_out_Q")
reference_dir = os.path.join(base_dir, test_reference, "sample_ref")
os.system("rm -rf " + output_dir)
#subprocess.Popen(["EUKulele", "setup", "--database", "mmetsp", "--sample_dir", sample_dir,
# "--mets_or_mags", "mets", "--out_dir", output_dir,
# "--reference_dir", reference_dir])
string_arguments = " ".join([
"setup", "--database", "mmetsp", "--sample_dir", sample_dir,
"--mets_or_mags", "mets", "--out_dir", output_dir, "--ref_fasta",
"reference.pep.fa", "--reference_dir", reference_dir
])
eukulele(string_arguments=string_arguments)
assert os.path.isfile(os.path.join(reference_dir, "tax-table.txt"))
def test_error_required_input():
base_dir = os.path.join(os.path.dirname(__file__), '..', 'aux_data')
sample_dir = os.path.join(base_dir, test_reference, "samples_MAGs")
output_dir = os.path.join(base_dir, "test_out_G")
os.system("rm -rf " + output_dir)
reference_dir = os.path.join(base_dir, test_reference, "sample_ref")
string_arguments = " ".join(["--database", "mmetsp", "--sample_dir", sample_dir,
"--out_dir", output_dir, "-i",
'--organisms', 'Chromera', '--taxonomy_organisms', 'genus',
"--reference_dir", reference_dir])
error = 0
try:
eukulele(string_arguments=string_arguments)
except:
error = 1
assert error == 1
def test_setup():
'''
Tests the setup subroutine within EUKulele.
'''
base_dir = os.path.join(os.path.dirname(__file__), '..', 'aux_data')
base_config = os.path.join(os.path.dirname(__file__), '..', 'aux_data',
'config.yaml')
with open(base_config) as f:
config = yaml.load(f, Loader=yaml.FullLoader)
config["mets_or_mags"] = "mags"
config["reference"] = os.path.join(base_dir, test_reference,
"sample_ref_MAG")
config["samples"] = os.path.join(base_dir, test_reference, "samples_MAGs")
config["subroutine"] = "setup"
config["output"] = os.path.join(base_dir, "test_out_A")
config["database"] = test_reference
config["download_reference"] = 0
config["column"] = "SOURCE_ID"
config["ref_fasta"] = "reference.pep.fa"
config["protein_map"] = "prot-map.json"
config["tax_table"] = "tax-table.txt"
config_path = os.path.join(base_dir, 'test_configs')
os.system("mkdir -p " + config_path)
os.system("rm -rf " + config["output"])
config_file = os.path.join(config_path, 'curr_config_setup.yaml')
with open(config_file, 'w') as f:
yaml.dump(config, f)
eukulele(config=config_file)
assert os.path.isfile(
os.path.join(config["reference"], config["tax_table"]))
config["subroutine"] = "alignment"
with open(config_file, 'w') as f:
yaml.dump(config, f)
eukulele(config=config_file)
outprefix = config["output"].split("/")[-1]
assert os.path.isfile(
os.path.join(config["output"], "taxonomy_counts",
outprefix + "_all_species_counts.csv"))
def test_tester():
'''
Tests the setup of the tests.
'''
base_dir = os.path.join(os.path.dirname(__file__), '..', 'aux_data')
sample_dir = os.path.join(base_dir, test_reference, "samples_MAGs")
output_dir = os.path.join(base_dir, "test_out")
reference_dir = os.path.join(base_dir, test_reference, "sample_ref")
os.system("rm -rf " + output_dir)
string_arguments = " ".join([
"setup", "--test", "--database", "mmetsp", "--sample_dir", sample_dir,
"--mets_or_mags", "mags", "--out_dir", output_dir, "--ref_fasta",
"reference.pep.fa", "--reference_dir", reference_dir
])
eukulele(string_arguments=string_arguments)
assert (not os.path.isdir(output_dir))
def test_all_commandline_busco_individual():
"""
Tests that BUSCO runs using arguments provided as a string.
"""
base_dir = os.path.join(os.path.dirname(__file__), '..', 'aux_data')
sample_dir = os.path.join(base_dir, test_reference, "samples_METs_small")
output_dir = os.path.join(base_dir, "test_out_T")
reference_dir = os.path.join(base_dir, test_reference, "sample_ref")
string_arguments = [
"setup", "--database", "mmetsp", "--sample_dir", sample_dir,
"--mets_or_mags", "mets", "--out_dir", output_dir,
"--individual_or_summary", "individual", '--organisms', 'Chromera',
'--taxonomy_organisms', 'genus', "--ref_fasta", "reference.pep.fa",
"--reference_dir", reference_dir
]
eukulele(string_arguments=" ".join(string_arguments))
string_arguments[0] = "alignment"
eukulele(string_arguments=" ".join(string_arguments))
string_arguments[0] = "busco"
eukulele(string_arguments=" ".join(string_arguments))
samplenames = [curr.split(".")[0] for curr in os.listdir(sample_dir)]
busco_out = os.path.join(output_dir, "busco_assessment", samplenames[0],
"individual",
"summary_" + samplenames[0] + ".tsv")
#busco_out = os.path.join(output_dir, "busco_assessment", samplenames[0],
# "species_combined", "summary_species_" + samplenames[0] + ".tsv")
assert os.path.isfile(busco_out)
def test_error_input():
'''
Checking that we can catch an expected error in the input formatting.
'''
base_dir = os.path.join(os.path.dirname(__file__), '..', 'aux_data')
sample_dir = os.path.join(base_dir, test_reference, "samples_MAGs")
output_dir = os.path.join(base_dir, "test_out_F")
os.system("rm -rf " + output_dir)
reference_dir = os.path.join(base_dir, test_reference, "sample_ref_MAGs")
string_arguments = " ".join([
"--database", "mmetsp", "--sample_dir", sample_dir, "--mets_or_mags",
"mmm", "--out_dir", output_dir, "-i", '--organisms', 'Chromera',
'--taxonomy_organisms', 'genus', "--reference_dir", reference_dir
])
error = 0
try:
eukulele(string_arguments=string_arguments)
except:
error = 1
assert error == 1
def test_error_p_extension():
'''
Tests that we get an error when we use an improper protein
extension for the files.
'''
base_dir = os.path.join(os.path.dirname(__file__), '..', 'aux_data')
sample_dir = os.path.join(base_dir, test_reference, "samples_MAGs")
output_dir = os.path.join(base_dir, "test_out_J")
os.system("rm -rf " + output_dir)
reference_dir = os.path.join(base_dir, test_reference, "sample_ref")
string_arguments = " ".join([
"--database", "mmetsp", "--sample_dir", sample_dir, "--mets_or_mags",
"mags", "--out_dir", output_dir, "-i", "--p_ext", ".hello",
"--reference_dir", reference_dir
])
error = 0
try:
eukulele(string_arguments=string_arguments)
except:
error = 1
assert error == 1
def test_setup():
base_dir = os.path.join(os.path.dirname(__file__), '..', 'aux_data')
base_config = os.path.join(os.path.dirname(__file__), '..', 'aux_data',
'config.yaml')
base_config_curr = os.path.join(os.path.dirname(__file__), '..',
'aux_data', 'config_P.yaml')
os.system("cp " + base_config + " " + base_config_curr)
with open(base_config_curr) as f:
config = yaml.load(f, Loader=yaml.FullLoader)
outputdir = os.path.join(base_dir, "test_out_P")
os.system("rm -rf " + outputdir)
config["mets_or_mags"] = "mets"
config["reference"] = os.path.join(base_dir, test_reference, "sample_ref")
config["samples"] = os.path.join(base_dir, test_reference,
"samples_METs_small")
config["subroutine"] = "setup"
config["output"] = outputdir
config["database"] = test_reference
config["download_reference"] = 0
config["column"] = "SOURCE_ID"
config["nucleotide_extension"] = ".fasta"
config["ref_fasta"] = "reference.pep.fa"
config["protein_map"] = "prot-map.json"
config["tax_table"] = "tax-table.txt"
config_path = os.path.join(base_dir, 'test_configs')
os.system("mkdir -p " + config_path)
config_file = os.path.join(config_path, 'curr_config_setup_P.yaml')
with open(config_file, 'w') as f:
yaml.dump(config, f)
eukulele(config=config_file)
assert os.path.isfile(
os.path.join(config["reference"], config["tax_table"]))
