def test_summarize_sample_info():
# run summarize_sample_info
global _tempdir
conf = utils.relative_file('tests/test-data/SRR5950647_subset.conf')
test_data = utils.relative_file("tests/test-data")
extra_args = ["summarize_sample_info"]
status = run_snakemake(
conf,
verbose=True,
outdir=_tempdir,
extra_args=extra_args,
)
assert status == 0
info_file = f"{_tempdir}/SRR5950647_subset.info.yaml"
assert os.path.exists(info_file)
with open(info_file, 'rt') as fp:
info = yaml.safe_load(fp)
print('XXX', info)
#{'kmers': 928685, 'known_hashes': 807, 'n_bases': 2276334, 'n_reads': 24663, 'sample': 'HSMA33MX-subset', 'total_hashes': 907, 'unknown_hashes': 100}
assert info['kmers'] == 928685
assert info['sample'] == 'SRR5950647_subset'
assert info['known_hashes'] == 653
assert info['n_bases'] == 2276334
assert info['n_reads'] == 24663
assert info['total_hashes'] == 907
assert info['unknown_hashes'] == 254
def test_smash_sig():
# run 'smash_reads'
global _tempdir
abundtrim_dir = os.path.join(_tempdir, "abundtrim")
os.mkdir(abundtrim_dir)
conf = utils.relative_file('tests/test-data/SRR5950647_subset.conf')
src = utils.relative_file("tests/test-data/SRR5950647_subset.abundtrim.fq.gz")
shutil.copy(src, abundtrim_dir)
extra_args = ["smash_reads"]
status = run_snakemake(
conf,
verbose=True,
outdir=_tempdir,
extra_args=extra_args,
)
assert status == 0
output_sig = f"{_tempdir}/sigs/SRR5950647_subset.abundtrim.sig.zip"
assert os.path.exists(output_sig)
sigs = list(sourmash.load_file_as_signatures(output_sig))
assert len(sigs) == 3
for s in sigs:
assert s.minhash.track_abundance
def test_bad_config_2():
# check for presence of 'sample' instead of 'samples', old config
global _tempdir
conf = utils.relative_file('tests/test-data/bad-2.conf')
status = run_snakemake(conf, verbose=True, outdir=_tempdir,
extra_args=["check"])
assert status != 0
def test_bad_config_1():
# check for presence of sourmash_database_glob_pattern, old config
global _tempdir
conf = utils.relative_file('tests/test-data/bad-1.conf')
status = run_snakemake(conf, verbose=True, outdir=_tempdir,
extra_args=["check"])
assert status != 0
def test_bad_config_4():
# check for presence of 'taxonomies' as a string, not a list.
# old config
global _tempdir
conf = utils.relative_file('tests/test-data/bad-4.conf')
status = run_snakemake(conf, verbose=True, outdir=_tempdir,
extra_args=["check"])
assert status != 0
def test_bad_config_3():
# check for presence of 'database_taxonomy' instead of 'taxonomies',
# old config
global _tempdir
conf = utils.relative_file('tests/test-data/bad-3.conf')
status = run_snakemake(conf, verbose=True, outdir=_tempdir,
extra_args=["check"])
assert status != 0
def test_block_sra_downloads():
# run 'smash_reads' with a non-existent metagenome file & make sure
# that it doesn't work.
global _tempdir
conf = utils.relative_file('tests/test-data/test-block-sra.conf')
extra_args = ["smash_reads"]
status = run_snakemake(
conf,
verbose=True,
outdir=_tempdir,
extra_args=extra_args,
)
assert status != 0
def test_map_reads():
global _tempdir
conf = utils.relative_file('tests/test-data/SRR5950647_subset.conf')
test_data = utils.relative_file("tests/test-data")
genomes_dir = os.path.join(_tempdir, "genomes")
os.mkdir(genomes_dir)
extra_args = ["map_reads", "-j", "4"]
status = run_snakemake(
conf,
verbose=True,
outdir=_tempdir,
extra_args=extra_args,
)
assert status == 0
def test_gather_to_tax():
# run gather_to_tax
global _tempdir
conf = utils.relative_file('tests/test-data/SRR5950647_subset.conf')
test_data = utils.relative_file("tests/test-data")
extra_args = ["gather_to_tax"]
status = run_snakemake(
conf,
verbose=True,
outdir=_tempdir,
extra_args=extra_args,
)
assert status == 0
tax_output = f"{_tempdir}/gather/SRR5950647_subset.gather.with-lineages.csv"
assert os.path.exists(tax_output)
tax_results = list(utils.load_csv(tax_output))
assert len(tax_results) == 2
def test_gather_reads_with_picklist():
# check gather with picklist
global _tempdir
conf = utils.relative_file('tests/test-data/SRR5950647_picklist.conf')
test_data = utils.relative_file("tests/test-data")
# note: the prefetch command & CSV are what are actually limited by the
# passed in picklist.
prefetch_output = f"{_tempdir}/gather/SRR5950647_subset.prefetch.csv"
if os.path.exists(prefetch_output):
os.unlink(prefetch_output)
gather_output = f"{_tempdir}/gather/SRR5950647_subset.gather.csv"
if os.path.exists(gather_output):
os.unlink(gather_output)
extra_args = ["gather_reads"]
status = run_snakemake(
conf,
verbose=True,
outdir=_tempdir,
extra_args=extra_args,
)
assert status == 0
assert os.path.exists(gather_output)
prefetch_results = list(utils.load_csv(prefetch_output))
assert len(prefetch_results) == 1
assert prefetch_results[0]['match_name'].startswith('GCF_902167755.1 ')
gather_results = list(utils.load_csv(gather_output))
assert len(gather_results) == 1
assert gather_results[0]['name'].startswith('GCF_902167755.1 ')
# make sure the picklist version of the CSVs is cleaned up!
os.unlink(prefetch_output)
os.unlink(gather_output)
