def __init__(self, genome_name="chM", sample_name="SAMP_CHM"):
"""
Empty databases prior to start
:return:
"""
sync_test_data()
db.fastqs.drop()
db.mappings.drop()
db.experiments.drop()
db.gtfs.drop()
mock_insert(sample_name, genome_name)
gtfs.get_version_before = Mock(return_value=genome_name)
encode.get_online_list = Mock(
return_value=ex_mock.get_online_list(sample_name))
self.e_acc = sample_name
self.gtf_ver = gtfs.get_version_before(datetime.datetime.now())
self.design_dir = os.path.join(config.results_root, "junctionseq",
self.gtf_ver, self.e_acc)
self.design_by_sample = os.path.join(self.design_dir,
"decoder.bySample.txt")
self.design_by_uid = os.path.join(self.design_dir, "decoder.byUID.txt")
# Design files need to be generated inside the tests
if os.path.exists(self.design_dir):
print("Directory %s exists, removing ..." % self.design_dir)
shutil.rmtree(self.design_dir)
def setUp(self):
db.gtfs.drop()
self.gtf_ver = gtfs.get_version_before(datetime.datetime.min)
self.in_gtf = gtfs.version_to_path(gtf_ver=self.gtf_ver)
self.in_gff = gtfs.version_to_path(gtf_ver=self.gtf_ver, gff=True)
self.genome_dir = gtfs.get_genome_index_dir(self.gtf_ver)
if os.path.exists(self.in_gff):
os.remove(self.in_gff)
def test_count_bam(self):
# Test counting functionality base on recieved data
empty_and_create(in_dir=self.out_count_dir)
in_gtf = gtfs.version_to_path(gtfs.get_version_before(
datetime.MINYEAR))
in_bam = os.path.join(self.out_mapping_dir, mappings.STAR_BAM_NAME)
mappings.count_bam(in_bam, in_gtf, self.out_count_dir, None)
assert os.path.exists(
os.path.join(self.out_count_dir, mappings.QORTS_COUNT_NAME))
def test_process_queue(self):
# Insert data on fastqs into database
in_gtf = gtfs.get_version_before(datetime.MINYEAR)
out_bam = mappings.get_bam_file_paths(self.fastq_pair, in_gtf)
assert out_bam is None
# Assert correct insertion and directory creation
lst = list(
db.mappings.find({
"fastq_pair": self.fastq_pair,
"gtf_ver": in_gtf,
"status": "to map"
}))
assert len(lst) == 1
out_bam_dir = lst[0]["out_dir"]
out_count_dir = lst[0]["out_count_dir"]
empty_and_create(out_bam_dir)
empty_and_create(out_count_dir)
# Run mapping and counting jobs by the same process method;
# first run is map, next run is count
for upcoming_status in ["to count", "ready"]:
mappings.process()
lst = []
while len(lst) == 0:
lst = list(
db.mappings.find({
"fastq_pair": self.fastq_pair,
"gtf_ver": in_gtf,
"status": upcoming_status
}))
time.sleep(1)
print("Current record", lst)
# Check that results exist and paths are correct
assert os.path.exists(os.path.join(out_bam_dir,
mappings.STAR_BAM_NAME))
assert os.path.exists(
os.path.join(out_count_dir, mappings.QORTS_COUNT_NAME))
# Assert read count is correctly written to database
rec = lst[0]
assert rec["read_count"] != -1
def setUp(self):
self.gtf_ver = gtfs.get_version_before(datetime.datetime.now())
self.in_gtf = gtfs.version_to_path(self.gtf_ver)