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import sys
THRESHOLD = 0.25 # reads must have 25% of their k-mers assigned
for line in sys.stdin:
fields = line.strip().split()
kmers_fields = fields[4:]
total_kmers = sum([int(x.split(":")[1]) for x in kmers_fields])
unassigned_kmers = sum([int(x.split(":")[1]) for x in kmers_fields if x[0] == "0"])
if total_kmers == 0:
# Drop unassigned results
elif unassigned_kmers / float(total_kmers) > (1.0 - THRESHOLD):
# Drop reads with many unassigned k-mers
# Elsewise, print the read to stdout
print (line.strip())

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@DesmondoDekker DesmondoDekker commented Oct 23, 2018

Hey hey,
your script seems really useful.
I have only a concern about what to use as input file...Do you have some instructions more about this script?

Alle the best


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