kraken-lonelykmers.py

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
        continue
     elif unassigned_kmers / float(total_kmers) > (1.0 - THRESHOLD):
        # Drop reads with many unassigned k-mers
        continue
       
    # Elsewise, print the read to stdout
     print (line.strip())

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

Luigi