def main():
args = getArgs()
key = encodedcc.ENC_Key(args.keyfile, args.key)
connection = encodedcc.ENC_Connection(key)
accessions = []
if args.infile:
accessions = [line.rstrip("\n") for line in open(args.infile)]
elif args.query:
data = encodedcc.get_ENCODE(args.query, connection).get("@graph", [])
for exp in data:
files = exp.get("files", [])
for f in files:
res = encodedcc.get_ENCODE(f, connection)
f_type = res.get("file_format", "")
if f_type == "fastq":
accessions.append(res["accession"])
elif args.accession:
accessions = [args.accession]
else:
print("No accessions to check")
sys.exit(1)
for acc in accessions:
link = "/files/" + acc + "/@@download/" + acc + ".fastq.gz"
for header, sequence, qual_header, quality in encodedcc.fastq_read(connection, uri=link):
if args.header:
header = header.decode("UTF-8")
print(header)
else:
sequence = sequence.decode("UTF-8")
print(acc + "\t" + str(len(sequence)))
def process_row(row, connection):
json_payload = {}
flowcell_dict = {}
if row.get("file_format", "") == "fastq":
for header, sequence, qual_header, quality in encodedcc.fastq_read(
connection, filename=row["submitted_file_name"]):
sequence = sequence.decode("UTF-8")
read_length = len(sequence)
json_payload.update({"read_length": read_length})
for key in row.keys():
k = key.split(":")
if k[0] in ["flowcell", "machine", "lane", "barcode"]:
flowcell_dict[k[0]] = row[k[0]]
else:
if len(k) > 1:
if k[1] in ["int", "integer"]:
value = int(row[key])
elif k[1] in ["list", "array"]:
value = row[key].strip("[]").split(",")
else:
value = row[key]
if not k[0]:
continue
try:
if type(value) == list:
json_payload.update({k[0]: value})
else:
json_payload.update({k[0]: json.loads(value)})
except:
try:
json_payload.update({k[0]: json.loads('"%s"' % (value))})
except:
logger.warning(
'Could not convert field %s value %s to JSON' %
(k[0], value))
return None
if any(flowcell_dict):
flowcell_list = [flowcell_dict]
json_payload.update({"flowcell_details": flowcell_list})
if type(json_payload.get("paired_end")) == int:
if json_payload["paired_end"] == 1:
json_payload.pop("paired_with", None)
json_payload["paired_end"] = str(json_payload["paired_end"])
print(json_payload)
return json_payload
def process_row(row, connection):
json_payload = {}
flowcell_dict = {}
if row.get("file_format", "") == "fastq":
for header, sequence, qual_header, quality in encodedcc.fastq_read(connection, filename=row["submitted_file_name"]):
sequence = sequence.decode("UTF-8")
read_length = len(sequence)
json_payload.update({"read_length": read_length})
for key in row.keys():
k = key.split(":")
if k[0] in ["flowcell", "machine", "lane", "barcode"]:
flowcell_dict[k[0]] = row[k[0]]
else:
if len(k) > 1:
if k[1] in ["int", "integer"]:
value = int(row[key])
elif k[1] in ["list", "array"]:
value = row[key].strip("[]").split(",")
else:
value = row[key]
if not k[0]:
continue
try:
if type(value) == list:
json_payload.update({k[0]: value})
else:
json_payload.update({k[0]: json.loads(value)})
except:
try:
json_payload.update({k[0]: json.loads('"%s"' % (value))})
except:
logger.warning('Could not convert field %s value %s to JSON' % (k[0], value))
return None
if any(flowcell_dict):
flowcell_list = [flowcell_dict]
json_payload.update({"flowcell_details": flowcell_list})
if type(json_payload.get("paired_end")) == int:
if json_payload["paired_end"] == 1:
json_payload.pop("paired_with", None)
json_payload["paired_end"] = str(json_payload["paired_end"])
print(json_payload)
return json_payload
def main():
args = getArgs()
key = encodedcc.ENC_Key(args.keyfile, args.key)
connection = encodedcc.ENC_Connection(key)
accessions = []
if args.infile:
if os.path.isfile(args.infile):
accessions = [line.strip() for line in open(args.infile)]
else:
accessions = args.infile.split(",")
elif args.query:
data = []
if "search" in args.query:
data = encodedcc.get_ENCODE(args.query,
connection).get("@graph", [])
else:
data = [encodedcc.get_ENCODE(args.query, connection)]
for exp in data:
files = exp.get("files", [])
for f in files:
res = encodedcc.get_ENCODE(f, connection)
f_type = res.get("file_format", "")
if f_type == "fastq":
accessions.append(res["accession"])
else:
print("No accessions to check")
sys.exit(1)
for acc in accessions:
link = "/files/" + acc + "/@@download/" + acc + ".fastq.gz"
for header, sequence, qual_header, quality in encodedcc.fastq_read(
connection, uri=link):
if args.header:
header = header.decode("UTF-8")
print(acc + "\t" + str(len(sequence)) + "\t" + header)
else:
sequence = sequence.decode("UTF-8")
print(acc + "\t" + str(len(sequence)))
