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mkweskin/avgQseq

Created April 6, 2017 19:00
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Gives the average Q value for each sequence in a fastq
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avgQseq
#!/usr/bin/env python
import numpy as np
from Bio import SeqIO
for record in SeqIO.parse("test_R1.fq", "fastq"):
print ('{}\t{}'.format(record.id, np.mean(record.letter_annotations["phred_quality"])))
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