def create_or_update(self, key, value):
record = Record(key, value, type(value))
if self.pipe:
self.in_memory_db[key] = record
else:
file_path = self.dbcore.get_file_path(key)
self.dbcore.write(file_path, record)
return record
def test_read_write(self):
key = str(uuid.uuid4())
value = "test"
dbcore = DbCore()
record = Record(key, value, type(value))
folder_path = dbcore.get_file_path(key)
dbcore.write(folder_path, record)
assert dbcore.read(folder_path).value == value
dbcore.delete(folder_path)
def test_delete(self):
key = str(uuid.uuid4())
value = "test"
dbcore = DbCore()
record = Record(key, value, type(value))
folder_path = dbcore.get_file_path(key)
dbcore.write(folder_path, record)
dbcore.delete(folder_path)
try:
dbcore.read(folder_path)
except FileNotFoundError:
assert True
def run(self):
if options.args['logfile']:
logging.info('Process ' + str(self.threadidx) +
' - variant annotation started.')
# Iterating through input file
counter = 0
thr = 10
for line in self.infile:
counter += 1
# Considering lines between startline and endline only
if counter < int(self.startline): continue
if not self.endline == '':
if counter > int(self.endline): break
line = line.strip()
if line == '': continue
# Printing out progress information
if not copts.stdout and self.threadidx == 1:
if counter % 1000 == 0:
printProgressInfo(
counter, int(self.numOfRecords / self.copts.threads))
# Parsing record from input file
record = Record(line, self.options, self.targetBED)
# Filtering out REFCALL records
if record.filter == 'REFCALL': continue
# Filtering record, if required
if self.options.args['filter'] and not record.filter == 'PASS':
continue
# Only include records of allowed chromosome names
if record.chrom not in self.chroms: continue
# Annotating the record based on the Ensembl, dbSNP and reference data
record.annotate(self.ensembl, self.dbsnp, self.reference,
self.impactdir)
# Writing annotated record to output file
record.output(self.options.args['outputformat'], self.outfile,
self.options, self.genelist, self.transcriptlist,
self.snplist, self.copts.stdout)
# Writing progress information to log file
if self.threadidx == 1 and self.options.args['logfile']:
x = round(
100 * counter /
int(self.numOfRecords / self.copts.threads), 1)
x = min(x, 100.0)
if x > thr:
logging.info(str(thr) + '% of records annotated.')
thr += 10
# Closing output file
self.outfile.close()
# Finalizing progreaa info
if not copts.stdout and self.threadidx == 1: finalizeProgressInfo()