def test_random_value():
r = RandomDict()
for i in range(10000):
r[i] = i
values = set(range(10000))
for i in range(100000):
assert r.random_value() in values
print('Writing sim data to file.')
count = 1
with open(args.Outputname + "_R1.fastq",
"w") as handleR1, open(args.Outputname + "_R2.fastq",
"w") as handleR2:
for myfile in args.T:
record_dict = SeqIO.index(myfile.name, "fasta")
record_rand = RandomDict(record_dict)
for cell in range(0, nrCells):
cellSeq = random.sample(cell_pool, 1)[0]
cell_pool.discard(cellSeq)
umi_set = generate_umi_set(args.umi_bc_length, 100, 0.2)
for record in range(0, nrSeqs):
UMIseq = random.sample(umi_set, 1)[0]
myItem = record_rand.random_value()
if random.random() < 0.01:
myItem.seq = Seq(
mutate(sequence=myItem.seq, mutation_rate=0.001))
myItem += "A" * 150
start = 0
#print(myItem.id + " length: " + str(limit))
end = start + myLength
mySub = myItem[start:end]
seqid = myItem.id + ":" + cellSeq + ":" + UMIseq + ":" + str(
count)
mySub.id = seqid + "/2"
mySub.letter_annotations["phred_quality"] = [24] * len(mySub)
tmp = SeqIO.write(mySub, handleR2, "fastq")
mySub2 = SeqRecord(Seq(cellSeq + UMIseq),
def test_empty_random_value():
r = RandomDict()
r.random_value()