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I have a Fastq file and I want to get the exact count of each possible kmer from this file.

On a previous post called How to use khmer to count k-mers? Daniel Standage proposed a custom script based on khmer methods that you can see down below :

>>> outfile = open('outfile.txt', 'w') 
>>> seenkmers = set()  # Consumes a lot of memory for large input!!!
>>> for read in khmer.ReadParser('reads.fq.gz'):
...     for kmer in counts.get_kmers(read.sequence):
...         if kmer not in seenkmers:
...             print(kmer, counttable.get(kmer), file=outfile)
...             seenkmers.add(kmer)

The code works if I switch counttable.get(kmer) with count.get(kmer) but the main problem is that when I try on a customized fastq file with 300 occurrences of one kmer, the count will still be stuck at 255 and can't go further, and for some reason I can't pass through this limit.

Is this coming from the minimum table size ?

Does anyone know if there is a parameter that can work on a custom script to disable this limit ?

I have a Fastq file and I want to get the exact count of each possible kmer from this file.

On a previous post called How to use khmer to count k-mers? Daniel Standage proposed a custom script based on khmer methods that you can see down below :

>>> outfile = open('outfile.txt', 'w') 
>>> seenkmers = set()  # Consumes a lot of memory for large input!!!
>>> for read in khmer.ReadParser('reads.fq.gz'):
...     for kmer in counts.get_kmers(read.sequence):
...         if kmer not in seenkmers:
...             print(kmer, counttable.get(kmer), file=outfile)
...             seenkmers.add(kmer)

The code works if I switch counttable.get(kmer) with counts.get(kmer) but the main problem is that when I try on a customized fastq file with 300 occurrences of one kmer, the count will still be stuck at 255 and can't go further, and for some reason I can't pass through this limit.

Is this coming from the minimum table size ?

Does anyone know if there is a parameter that can work on a custom script to disable this limit ?

I have a Fastq file and i want to get the exact count of each possible kmer from this file.

On a previous post called How to use khmer to count k-mers? Daniel Standage proposed a custom script based on khmer methods that you can see down below :

>>> outfile = open('outfile.txt', 'w') 
>>> seenkmers = set()  # Consumes a lot of memory for large input!!!
>>> for read in khmer.ReadParser('reads.fq.gz'):
...     for kmer in counts.get_kmers(read.sequence):
...         if kmer not in seenkmers:
...             print(kmer, counttable.get(kmer), file=outfile)
...             seenkmers.add(kmer)

The code works if i switch counttable.get(kmer) with count.get(kmer) but the main problem is that when i try on a customized fastqfile with 300 occurences of one kmer the count will still be stuck at 255 and can't go further and for some reason i can't pass through this limit.

Is this coming from the minimun table size ?

Does anyone know if there is a parameter that can work on a custom script to disable this limit ?

I have a Fastq file and I want to get the exact count of each possible kmer from this file.

On a previous post called How to use khmer to count k-mers? Daniel Standage proposed a custom script based on khmer methods that you can see down below :

>>> outfile = open('outfile.txt', 'w') 
>>> seenkmers = set()  # Consumes a lot of memory for large input!!!
>>> for read in khmer.ReadParser('reads.fq.gz'):
...     for kmer in counts.get_kmers(read.sequence):
...         if kmer not in seenkmers:
...             print(kmer, counttable.get(kmer), file=outfile)
...             seenkmers.add(kmer)

The code works if I switch counttable.get(kmer) with count.get(kmer) but the main problem is that when I try on a customized fastq file with 300 occurrences of one kmer, the count will still be stuck at 255 and can't go further, and for some reason I can't pass through this limit.

Is this coming from the minimum table size ?

Does anyone know if there is a parameter that can work on a custom script to disable this limit ?