def simple_index_parser (self):
# Iterate over fastq chunks for sequence and index reads
for n, (R1, R2, I1) in enumerate (zip(self.seq_R1, self.seq_R2, self.index_R1)):
print("Start parsing chunk {}/{}".format(n+1, len(self.seq_R1)))
# Init FastqReader generators
R1_gen = FastqReader(R1)
R2_gen = FastqReader(R2)
I1_gen = FastqReader(I1)
# Iterate over reads in fastq files until exhaustion
try:
while True:
read1 = R1_gen.next()
read2 = R2_gen.next()
index1 = I1_gen.next()
# Extract index and molecular sequences from index reads
index = index1[self.idx1_pos["start"]:self.idx1_pos["end"]]
molecular = index1.seq[self.mol1_pos["start"]:self.mol1_pos["end"]]
# Identify sample and verify index quality
Sample.FINDER (read1,read2, index, molecular)
except StopIteration as E:
print(E)
print("\tEnd of chunk {}".format(n+1))
