def add_to_barcode(read, barcode):
latest_buf = barcode_bufs[barcode]
if len(latest_buf[0].reads) >= MAX_BUF_SIZE:
print("Writing file %d for %s" % (latest_buf[1], barcode))
with open("protobufs/%s_%i.protobuf" % (barcode, latest_buf[1]),
'wb') as output:
output.write(latest_buf[0].SerializeToString())
latest_buf = (reads_pb2.FakReads(), barcode_bufs[barcode][1] + 1)
barcode_bufs[barcode] = latest_buf
new_read = latest_buf[0].reads.add()
new_read.uuid = read.uuid
new_read.mod_base_probs = read.mod_base_probs
protobuf_files = []
read_ids = []
print("Looking for protobufs")
for filename in os.listdir(args.protobufs):
if not args.nonbarcoded:
if args.barcode in filename and ".protobuf" in filename:
protobuf_files.append(args.protobufs + filename)
else:
if ".protobuf" in filename:
protobuf_files.append(args.protobufs + filename)
print("Reading protobufs")
for protobuf_name in protobuf_files:
protobuf = open(protobuf_name, 'rb')
protobuf_reads = reads_pb2.FakReads()
protobuf_reads.ParseFromString(protobuf.read())
for index, read in enumerate(protobuf_reads.reads):
protobuf_index[read.uuid] = (protobuf_name, index)
read_ids.append(read.uuid)
protobuf.close()
# Import sacCer3 reference sequence as a dictionary
print("Importing {} reference sequence".format(genome_name))
genome_data = collections.OrderedDict()
with open(args.genome, "r") as ref_seq:
header = True
for line in ref_seq:
line = line.strip("\n")
if line.startswith(">"):
if not header:
if ".fast5" in entry:
filenames.append(entry)
print(filenames)
print(len(filenames))
# Check if any fast5 files were found and only continue if some were
if len(filenames) == 0:
print("Error: Filenames length is zero")
sys.exit()
# Iterate through a list of filenames of the fast5 files currently in the directory
for file in filenames:
reads = reads_pb2.FakReads()
file = file.split('.')[0]
print(file)
count_fast5 = 0
count_proto = 0
with get_fast5_file(file + ".fast5") as f5:
count_fast5 = len(f5.get_read_ids())
for read_id in f5.get_read_ids():
read = f5.get_read(read_id)
latest_basecall = read.get_latest_analysis("Basecall_1D")
mod_base_table = read.get_analysis_dataset(
latest_basecall, "BaseCalled_template/ModBaseProbs")
read = reads.reads.add()
read.uuid = read_id
import sys
import reads_pb2
import os
MAX_BUF_SIZE = 1000
barcode_bufs = {
"unclassified": (reads_pb2.FakReads(), 0),
"barcode01": (reads_pb2.FakReads(), 0),
"barcode02": (reads_pb2.FakReads(), 0),
"barcode03": (reads_pb2.FakReads(), 0),
"barcode04": (reads_pb2.FakReads(), 0),
"barcode05": (reads_pb2.FakReads(), 0),
"barcode06": (reads_pb2.FakReads(), 0),
"barcode07": (reads_pb2.FakReads(), 0),
"barcode08": (reads_pb2.FakReads(), 0),
"barcode09": (reads_pb2.FakReads(), 0),
"barcode10": (reads_pb2.FakReads(), 0),
"barcode11": (reads_pb2.FakReads(), 0),
"barcode12": (reads_pb2.FakReads(), 0),
"barcode13": (reads_pb2.FakReads(), 0),
"barcode14": (reads_pb2.FakReads(), 0),
"barcode15": (reads_pb2.FakReads(), 0),
"barcode16": (reads_pb2.FakReads(), 0),
"barcode17": (reads_pb2.FakReads(), 0),
"barcode18": (reads_pb2.FakReads(), 0),
"barcode19": (reads_pb2.FakReads(), 0),
"barcode20": (reads_pb2.FakReads(), 0),
"barcode21": (reads_pb2.FakReads(), 0),
"barcode22": (reads_pb2.FakReads(), 0),
"barcode23": (reads_pb2.FakReads(), 0),