def setUp(self):
pip_install_vtam_for_tests()
self.test_path = PathManager.get_test_path()
self.outdir_path = os.path.join(self.test_path, 'outdir')
pathlib.Path(self.outdir_path).mkdir(exist_ok=True, parents=True)
def setUpClass(cls):
########################################################################
#
# These tests need the vtam command in the path
#
########################################################################
pip_install_vtam_for_tests()
cls.package_path = os.path.join(PathManager.get_package_path())
cls.test_path = os.path.join(PathManager.get_test_path())
cls.outdir_path = os.path.join(cls.test_path, 'outdir')
cls.outdir_data_path = os.path.join(cls.outdir_path, 'data')
shutil.rmtree(cls.outdir_path, ignore_errors=True)
pathlib.Path(cls.outdir_data_path).mkdir(parents=True, exist_ok=True)
############################################################################################
#
# Download sorted reads dataset (Updated Oct 10, 2020)
#
############################################################################################
sorted_tar_path = os.path.join(cls.outdir_data_path, "sorted.tar.gz")
# Test first in local dir, otherwise in the remote URLs
if not os.path.isfile(sorted_tar_path) or pathlib.Path(
sorted_tar_path).stat().st_size < 1000000:
try:
# urllib.request.urlretrieve(sorted_tar_gz_url1, sorted_tar_path, MyProgressBar())
with tqdm(...) as t:
t.set_description(os.path.basename(sorted_tar_path))
urllib.request.urlretrieve(sorted_tar_gz_url1,
sorted_tar_path,
reporthook=tqdm_hook(t))
except Exception:
try:
# urllib.request.urlretrieve(sorted_tar_gz_url2, sorted_tar_path, MyProgressBar())
with tqdm(...) as t:
t.set_description(os.path.basename(sorted_tar_path))
urllib.request.urlretrieve(sorted_tar_gz_url2,
sorted_tar_path,
reporthook=tqdm_hook(t))
except Exception:
# urllib.request.urlretrieve(sorted_tar_gz_url3, sorted_tar_path, MyProgressBar())
with tqdm(...) as t:
t.set_description(os.path.basename(sorted_tar_path))
urllib.request.urlretrieve(sorted_tar_gz_url3,
sorted_tar_path,
reporthook=tqdm_hook(t))
tar = tarfile.open(sorted_tar_path, "r:gz")
tar.extractall(path=cls.outdir_data_path)
tar.close()
def setUpClass(cls):
# vtam needs to be in the tsv_path
pip_install_vtam_for_tests()
cls.test_path = os.path.join(PathManager.get_test_path())
cls.outdir_path = os.path.join(cls.test_path, 'outdir')
cls.args = {}
cls.args['taxonomy'] = os.path.join(cls.outdir_path, "taxonomy.tsv")
cls.args['coi_blast_db_dir'] = os.path.join(cls.outdir_path, "coi_blast_db_dir")
pathlib.Path(cls.args['coi_blast_db_dir']).mkdir(exist_ok=True, parents=True)
############################################################################################
#
# Run 'vtam taxonomy'
#
############################################################################################
cmd = "vtam taxonomy --output {taxonomy} --precomputed".format(**cls.args)
if sys.platform.startswith("win"):
args = cmd
else:
args = shlex.split(cmd)
subprocess.run(args=args)
############################################################################################
#
# Run 'vtam coi_blast_db'
#
############################################################################################
cmd = "vtam coi_blast_db --blastdbdir {coi_blast_db_dir} --blastdbname coi_blast_db_20200420 ".format(**cls.args)
# if not (os.path.isfile(os.path.join(cls.args['coi_blast_db_dir'], "coi_blast_db_20200420.nhr"))):
if sys.platform.startswith("win"):
args = cmd
else:
args = shlex.split(cmd)
subprocess.run(args=args)
def setUpClass(cls):
########################################################################
#
# These tests need the vtam command in the path
#
########################################################################
pip_install_vtam_for_tests() # vtam needs to be in the path
cls.package_path = PathManager.get_package_path()
cls.test_path = PathManager.get_test_path()
cls.outdir_path = os.path.join(cls.test_path, 'outdir')
shutil.rmtree(cls.outdir_path, ignore_errors=True)
cls.outdir_data_path = os.path.join(cls.outdir_path, 'data')
pathlib.Path(cls.outdir_data_path).mkdir(parents=True, exist_ok=True)
cls.outdir_download_path = os.path.join(cls.test_path,
'outdir_download')
pathlib.Path(cls.outdir_download_path).mkdir(parents=True,
exist_ok=True)
cls.snakefile_tuto_data = os.path.join(
cls.package_path, "data/snake.tuto.data_makeknownoccurrences.yml")
############################################################################################
#
# Set command args
#
############################################################################################
cls.args = {}
cls.args['package_path'] = cls.package_path
cls.args['snake_tuto_data'] = cls.snakefile_tuto_data
############################################################################################
#
# Download fastq test dataset
#
############################################################################################
fastq_tar_path = os.path.join(cls.outdir_download_path, "fastq.tar.gz")
# Test first in local dir, otherwise in the remote URLs
if not os.path.isfile(fastq_tar_path) or pathlib.Path(
fastq_tar_path).stat().st_size < 1000000:
try:
# urllib.request.urlretrieve(fastq_tar_gz_url1, fastq_tar_path, MyProgressBar())
with tqdm(...) as t:
t.set_description(os.path.basename(fastq_tar_path))
urllib.request.urlretrieve(fastq_tar_gz_url1,
fastq_tar_path,
reporthook=tqdm_hook(t))
except Exception:
try:
# urllib.request.urlretrieve(fastq_tar_gz_url2, fastq_tar_path, MyProgressBar())
with tqdm(...) as t:
t.set_description(os.path.basename(fastq_tar_path))
urllib.request.urlretrieve(fastq_tar_gz_url2,
fastq_tar_path,
reporthook=tqdm_hook(t))
except Exception:
# urllib.request.urlretrieve(fastq_tar_gz_url3, fastq_tar_path, MyProgressBar())
with tqdm(...) as t:
t.set_description(os.path.basename(fastq_tar_path))
urllib.request.urlretrieve(fastq_tar_gz_url3,
fastq_tar_path,
reporthook=tqdm_hook(t))
tar = tarfile.open(fastq_tar_path, "r:gz")
tar.extractall(path=cls.outdir_path)
tar.close()
############################################################################################
#
# Copy data to directory tree
#
############################################################################################
cmd = "snakemake --cores 1 -s {snake_tuto_data} --config MARKER=mfzr " \
"PROJECT=asper1 PACKAGE_PATH={package_path} --until all_one_marker_makeknownoccurrences".format(**cls.args)
if sys.platform.startswith("win"):
args = cmd
else:
args = shlex.split(cmd)
subprocess.run(args=args, check=True, cwd=cls.outdir_path)
def setUp(self):
pip_install_vtam_for_tests()
self.test_path = PathManager.get_test_path()
self.package_path = PathManager.get_package_path()
self.outdir_path = os.path.join(self.test_path, 'outdir')
shutil.rmtree(self.outdir_path, ignore_errors=True)
pathlib.Path(self.outdir_path).mkdir(parents=True, exist_ok=True)
self.args = {}
self.args['runmarker'] = os.path.join(self.package_path, "data",
"example", "pool_run_marker.tsv")
self.args['db'] = os.path.join(self.outdir_path, "db.sqlite")
############################################################################################
#
# Init DB
#
############################################################################################
filter_codon_stop_path = os.path.join(self.test_path,
"test_files_dryad.f40v5_small",
"run1_mfzr_zfzr",
"filter_codon_stop.tsv")
variant_path = os.path.join(self.test_path,
"test_files_dryad.f40v5_small",
"run1_mfzr_zfzr",
"variant_filter_codon_stop.tsv")
sample_information_path = os.path.join(self.test_path,
"test_files_dryad.f40v5_small",
"run1_mfzr_zfzr",
"sample_information.tsv")
self.engine = sqlalchemy.create_engine('sqlite:///{}'.format(
self.args['db']),
echo=False)
sample_information_df = pandas.read_csv(sample_information_path,
sep="\t",
header=0)
sample_information_df.to_sql(name=SampleInformation.__tablename__,
con=self.engine.connect(),
if_exists='replace')
run_df = pandas.DataFrame({'name': ['run1']}, index=range(1, 2))
run_df.to_sql(name=Run.__tablename__,
con=self.engine.connect(),
index_label='id',
if_exists='replace')
marker_df = pandas.DataFrame({'name': ['MFZR', 'ZFZR']},
index=range(1, 3))
marker_df.to_sql(name=Marker.__tablename__,
con=self.engine.connect(),
index_label='id',
if_exists='replace')
sample_df = pandas.DataFrame(
{'name': ['tpos1_run1', 'tnegtag_run1', '14ben01', '14ben02']},
index=range(1, 5))
sample_df.to_sql(name=Sample.__tablename__,
con=self.engine.connect(),
index_label='id',
if_exists='replace')
variant_df = pandas.read_csv(variant_path,
sep="\t",
header=0,
index_col='id')
variant_df.to_sql(name=Variant.__tablename__,
con=self.engine.connect(),
index_label='id',
if_exists='replace')
filter_codon_stop_df = pandas.read_csv(filter_codon_stop_path,
sep="\t",
header=0)
filter_codon_stop_df.to_sql(name=FilterCodonStop.__tablename__,
con=self.engine.connect(),
if_exists='replace')
filter_chimera_borderline_path = os.path.join(
self.test_path, "test_files_dryad.f40v5_small", "run1_mfzr_zfzr",
"filter_chimera_borderline_and_filter_codon_stop.tsv")
filter_chimera_borderline_db = pandas.read_csv(
filter_chimera_borderline_path, sep="\t", header=0)
filter_chimera_borderline_db.to_sql(
name=FilterChimeraBorderline.__tablename__,
con=self.engine.connect(),
if_exists='replace')
self.sample_list = ['tpos1_run1', 'tnegtag_run1', '14ben01', '14ben02']
def setUpClass(cls):
pip_install_vtam_for_tests() # vtam needs to be in the path
def setUpClass(cls):
pip_install_vtam_for_tests() # vtam needs to be in the path
cls.package_path = PathManager.get_package_path()
cls.test_path = os.path.join(PathManager.get_test_path())
cls.outdir_path = os.path.join(cls.test_path, 'outdir')
cls.outdir_data_path = os.path.join(cls.outdir_path, 'data')
shutil.rmtree(cls.outdir_path, ignore_errors=True
) # during development of the test, this prevents errors
pathlib.Path(cls.outdir_data_path).mkdir(parents=True, exist_ok=True)
############################################################################################
#
# Download fastq test dataset
#
############################################################################################
fastq_tar_path = os.path.join(cls.outdir_data_path, "fastq.tar.gz")
# Test first in local dir, otherwise in the remote URLs
if not os.path.isfile(fastq_tar_path) or pathlib.Path(
fastq_tar_path).stat().st_size < 1000000:
try:
# urllib.request.urlretrieve(fastq_tar_gz_url1, fastq_tar_path, MyProgressBar())
with tqdm(...) as t:
t.set_description(os.path.basename(fastq_tar_path))
urllib.request.urlretrieve(fastq_tar_gz_url1,
fastq_tar_path,
reporthook=tqdm_hook(t))
except Exception:
try:
# urllib.request.urlretrieve(fastq_tar_gz_url2, fastq_tar_path, MyProgressBar())
with tqdm(...) as t:
t.set_description(os.path.basename(fastq_tar_path))
urllib.request.urlretrieve(fastq_tar_gz_url2,
fastq_tar_path,
reporthook=tqdm_hook(t))
except Exception:
# urllib.request.urlretrieve(fastq_tar_gz_url3, fastq_tar_path, MyProgressBar())
with tqdm(...) as t:
t.set_description(os.path.basename(fastq_tar_path))
urllib.request.urlretrieve(fastq_tar_gz_url3,
fastq_tar_path,
reporthook=tqdm_hook(t))
tar = tarfile.open(fastq_tar_path, "r:gz")
tar.extractall(path=cls.outdir_path)
tar.close()
# Set test paths
cls.fastqinfo_path = os.path.join(PathManager.get_package_path(),
"data/example/fastqinfo.tsv")
cls.fastqdir_path = os.path.join(cls.outdir_path, "fastq")
cls.fastainfo_path = os.path.join(cls.outdir_path, "fastainfo.tsv")
cls.fastadir_path = os.path.join(cls.outdir_path, "merged")
cls.sorted_dir_path = os.path.join(cls.outdir_path, "sorted")
cls.sortedinfo_path = os.path.join(cls.sorted_dir_path,
"sortedinfo.tsv")
cls.log_path = os.path.join(cls.outdir_path, "vtam.log")
cls.asvtable_path = os.path.join(cls.outdir_path,
"asvtable_default.tsv")
cls.args = {}
cls.args['fastqinfo'] = cls.fastqinfo_path
cls.args['fastqdir'] = cls.fastqdir_path
cls.args['fastainfo'] = cls.fastainfo_path
cls.args['fastadir'] = cls.fastadir_path
cls.args['sorted'] = cls.sorted_dir_path
cls.args['db'] = os.path.join(cls.outdir_path, "db.sqlite")
cls.args['sortedinfo'] = cls.sortedinfo_path
cls.args['sorteddir'] = cls.sorted_dir_path
cls.args['asvtable'] = cls.asvtable_path
cls.args['log'] = cls.log_path
################################################################################################################
#
# Command Merge
#
################################################################################################################
cmd = "vtam merge --fastqinfo {fastqinfo} --fastqdir {fastqdir} --fastainfo {fastainfo} --fastadir {fastadir} " \
"-v --log {log}".format(**cls.args)
if sys.platform.startswith("win"):
args = cmd
else:
args = shlex.split(cmd)
subprocess.run(args=args)
def setUp(self):
pip_install_vtam_for_tests()
self.test_path = PathManager.get_test_path()
self.package_path = PathManager.get_package_path()
self.outdir_path = os.path.join(self.test_path, 'outdir')
shutil.rmtree(self.outdir_path, ignore_errors=True)
pathlib.Path(self.outdir_path).mkdir(exist_ok=True, parents=True)
marker_str = "id name\n1 IIICBR"
run_str = "id name\n1 TAS2"
sample_str = "id name\n1 S21"
variant_str = """id sequence
1 ATTGTCAGACACTCCGTACCATTAGGGTGCTGCAGTCGACTAGTCTATTTTAAGCTTACACGTAGCCGGAATTAGTTCATTACTGGGGTCAATTAATATCATAACAACGATCATTAACTAGAGGGCCCCAGGAATGACCTGGGAGAACTTACCGTTATTCGTGTGGGCTGTATTTATTACAGCGTGGTTACTTGTACTGTCTTTACCAGTACTAGCTGGTGCGATTACCATGCTGCTAACAGATAGGAACTAGAATACTAGTTTCTACGACCCGAACGGAGGAGGAGATCCTCTGCTATACCAGCATCTATTC"""
filter_indel_str = """id run_id marker_id variant_id sample_id replicate read_count filter_delete
1 1 1 1 1 1 50 0"""
from sqlalchemy import create_engine
db_path = os.path.join(self.outdir_path, 'db.sqlite')
self.engine = create_engine('sqlite:///{}'.format(db_path), echo=True)
from wopmars.Base import Base
Session = sqlalchemy.orm.sessionmaker(bind=self.engine)
self.session = Session()
Base.metadata.create_all(self.engine)
from io import StringIO
run_df = pandas.read_csv(StringIO(run_str), sep=" ")
run_df.to_sql(name=Run.__tablename__,
con=self.engine.connect(),
if_exists='append',
index=False)
marker_df = pandas.read_csv(StringIO(marker_str), sep=" ")
marker_df.to_sql(name=Marker.__tablename__,
con=self.engine.connect(),
if_exists='append',
index=False)
sample_df = pandas.read_csv(StringIO(sample_str), sep=" ")
sample_df.to_sql(name=Sample.__tablename__,
con=self.engine.connect(),
if_exists='append',
index=False)
filter_indel_df = pandas.read_csv(StringIO(filter_indel_str), sep=" ")
filter_indel_df.to_sql(name=FilterIndel.__tablename__,
con=self.engine.connect(),
if_exists='append',
index=False)
variant_df = pandas.read_csv(StringIO(variant_str), sep=" ")
variant_df.to_sql(name=Variant.__tablename__,
con=self.engine.connect(),
if_exists='append',
index=False)
pathlib.Path(os.path.join(self.outdir_path, "params.yml")).touch()
sortereadinfo_str = """run marker sample replicate sortedfasta
TAS2 IIICBR S21 1 TAS2-R1_S1_L001_R1_001_000.fasta"""
with open(os.path.join(self.outdir_path, "sortedinfo.tsv"),
'w') as fout:
fout.write(sortereadinfo_str)