kmer-map 0.0.1

A package for visualizing kmers.

Kmer Manifold Approximation and Projection (KMAP)

kmap is a package for visualizing kmers in 2D space.

Installation

conda create --name=kmap_test python=3.11
conda activate kmap_test
conda install anaconda::scipy
conda install anaconda::numpy
conda install anaconda::matplotlib
conda install anaconda::pandas
conda install anaconda::click
conda install anaconda::tomli-w
conda install anaconda::requests
conda install conda-forge::biopython
conda install bioconda::logomaker
pip install taichi

pip install kmer-map

Example usage

The following code shows the typical workflow of the test data in ./tests/test.fa

# step 0: preprocess input fast file
kmap preproc --fasta_file ./tests/test.fa --res_dir ./test 

# step 2: scanning for motifs 
kmap scan_motif --res_dir ./test --debug true

# step 3: visualize kmers
# now edit the "./test/config.toml" file, in the 3rd section "visualization"
# change "n_max_iter = 2500" to "n_max_iter = 100"  
kmap visualize_kmers --res_dir ./test --debug True

If you feel the consensus is AATCGATAGC, instead of A[AATCGATAGC]GA you can use the following commands. The motif logo for this consensus sequence is given by ./test/hamming_balls/logo.pdf

kmap ex_hamball --res_dir ./test --conseq AATCGATAGC --return_type matrix --output_file ./test/hamming_balls/AATCGATAGC_cntmat.csv 
kmap draw_logo --cnt_mat_numpy_file ./test/hamming_balls/AATCGATAGC_cntmat.csv --output_fig_file ./test/hamming_balls/logo.pdf

Or if you want to change the number of maximum mutations to the consensus sequence `` to 3, you can use the following commands to derive the motif. The motif logo for this consensus sequence is given by ./test/hamming_balls/logo.pdf

kmap ex_hamball --res_dir ./test --conseq GTACGTAGGTCCTA --return_type matrix --max_ham_dist 3 --output_file ./test/hamming_balls/GTACGTAGGTCCTA_cntmat.csv 
kmap draw_logo --cnt_mat_numpy_file ./test/hamming_balls/GTACGTAGGTCCTA_cntmat.csv --output_fig_file ./test/hamming_balls/logo.pdf