kmer_counter 0.2.0

Count kmers in regions or at SNVs or at indel breakpoints.

kmer_counter

Count kmers in regions or at SNVs or at indel breakpoints.

Requirements

kmer_counter requires Python 3.7 or above.

Installation

With pip:

pip install kmer_counter

With pipx:

pipx install --python python3.7 kmer_counter

Usage

Counting k-mers at SNVs

To count the 3-mers at SNVs do:

kmer_counter snv {genome}.2bit {snv_file}

Where the {snv_file} should be a vcf-like text file where the first four columns are: Chromosome, Position, Ref_Allele, Alt_Allele. Fx:

chr1  1000000  A G
chr1  1000200  G C
chr1  1000300  A T
chr1  1000500  C G

Comments or headers lines starting with "#" are allowed and will be ignored and any additional columns are also allowed but ignored. So a vcf file is also a valid input file. The Ref_Allele column should match the reference genome provided by the 2bit file. 2bit files can be downloaded from: https://hgdownload.cse.ucsc.edu/goldenpath/{genome}/bigZips/{genome}.2bit where {genome} is a valid UCSC genome assembly name (fx. "hg38").

Counting k-mers in genomic regions

Counting k-mers at indels