kmerPaPa

Tool to calculate a "k-mer pattern partition" from position specific k-mer counts. This can for instance be used to train a mutation rate model.

Requirements

kmerPaPa requires Python 3.8 or above.

Installation

kmerPaPa can be installed using pip:

pip install kmerpapa

or using pipx:

pipx install kmerpapa

Test data

The test data files used in the usage examples below can be downloaded from the test_data directory in the project's github repository:

wget https://github.com/BesenbacherLab/kmerPaPa/raw/main/test_data/mutated_5mers.txt
wget https://github.com/BesenbacherLab/kmerPaPa/raw/main/test_data/background_5mers.txt

Usage

If we want to train a mutation rate model then the input data should specifiy the number of times each k-mer is observed mutated and unmutated. One option is to have one file with the mutated k-mer counts (positive) and one file with the count of k-mers in the whole genome (background). We can then run kmerpapa like this:

kmerpapa --positive mutated_5mers.txt \
         --background background_5mers.txt \
         --penalty_values 3 5 7

The above command will first use cross validation to find the best penalty value between the values 3,5 and 7. Then it will find the optimal k-mer patter partiton using that penalty value. If both a list of penalty values and a list of pseudo-counts are specified then all combinations of values will be tested during cross validation:

kmerpapa --positive mutated_5mers.txt \
         --background background_5mers.txt \
         --penalty_values 3 5 6 \
         --pseudo_counts 0.5 1 10

If only a single combination of penalty_value and pseudo_count is provided then the default is not to run cross validation unless "--n_folds" option or the "CV_only" is used. The "CV_only" option can be used together with "--CVfile" option to parallelize grid search. Fx. using bash:

for c in 3 5 6; do
    for a in 0.5 1 10; do
        kmerpapa --positive mutated_5mers.txt \
         --background background_5mers.txt \
         --penalty_values $c \
         --pseudo_counts $a \
         --CV_only --CVfile CV_results_c${c}_a${a}.txt &
    done
done

Creating input data

Input files with k-mer counts can be created using kmer_counter. Given a file of point mutations in a file that contain the CHROM, POS, REF and ALT columns from a vcf file:

chr1 1000000 G A
chr1 1000100 G A
chr1 1000200 C T
chr1 1000300 C T
chr1 1000400 C T

We can count the 5-mers around each mutation using this command:

kmer_counter snv --radius 2 {genome}.2bit {point_mutations_file} > mutated_5mers.txt

Given a bed file with regions that are sufficiently covered by sequencing we can count the background 5-mers using this command:

kmer_counter background --bed {regions}.bed -radius 2 {genome}.2bit > background_5mers.txt

The file {genome}.2bit should be a 2bit file of the same reference genome that were used for calling the mutations. 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").