Created
August 24, 2018 17:03
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Extract UMIs from input fastq file
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from __future__ import print_function | |
import collections | |
import gzip | |
import sys | |
from Bio.SeqIO.QualityIO import FastqGeneralIterator | |
nbases = 15 | |
nreads = 1e6 | |
toshow = 20 | |
umis = collections.defaultdict(int) | |
with gzip.open(sys.argv[1]) as in_handle: | |
for i, (n, seq, q) in enumerate(FastqGeneralIterator(in_handle)): | |
umis[seq[:nbases]] += 1 | |
if i > nreads: | |
break | |
counts = [(c, u) for u, c in umis.items()] | |
counts.sort(reverse=True) | |
for i, (c, u) in enumerate(counts): | |
print(u, c) | |
if i > toshow: | |
break |
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