kcounter
A simple package for counting DNA k-mers in Python. Written in Rust.
Instalation
There are two ways to install kcounter:
- Using pip:
pip install kcounter
- Using conda:
conda install -c conda-forge -c bioconda kcounter
Usage
Currently, kcounter provides a single function, count_kmers, that returns a dictionary containing the k-mers of the chosen size.
>>> import kcounter
>>> kcounter.count_kmers('AAACTTTTTT', 3)
{'AAA': 1.0, 'ACT': 1.0, 'AAC': 1.0, 'CTT': 1.0, 'TTT': 4.0}
>>> kcounter.count_kmers('AAACTTTTTT', 4)
{'AACT': 1.0, 'CTTT': 1.0, 'ACTT': 1.0, 'AAAC': 1.0, 'TTTT': 3.0}
The relative_frequencies parameter can be used to obtain relative k-mer frequencies:
>>> kcounter.count_kmers('AAACTTTTTT', 3, relative_frequencies=True)
{'AAC': 0.125, 'TTT': 0.5, 'CTT': 0.125, 'ACT': 0.125, 'AAA': 0.125}
The canonical_kmers parameters aggregates the counts of reverse-complement k-mers (eg.: AGC/GCT):
>>> kcounter.count_kmers('AAACTTTTTT', 3, canonical_kmers=True)
{'ACT': 1.0, 'AAA': 5.0, 'AAC': 1.0, 'AAG': 1.0}
Plans for future versions:
- Performance improvements.
- Add an parameter that makes the function return a sparse k-mer counts.
- Implement a function that returns a numpy array.
1 maintainer
Metadata
1 maintainer
Release files for kcounter 0.1.2
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | Provenance | Actions |
|---|---|---|---|---|
| kcounter-0.1.2.tar.gz | 18.9 MB | Without provenance | Details for kcounter-0.1.2.tar.gz |
Built distributions (wheels)
Total release size: 37.8 MB
Release files / kcounter-0.1.2.tar.gz
| Download URL | kcounter-0.1.2.tar.gz |
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| Size | 18.9 MB |
| Tags | Source |
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twine/6.2.0 CPython/3.13.9
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Release files / kcounter-0.1.2-cp314-cp314-macosx_11_0_arm64.whl
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twine/6.2.0 CPython/3.13.9
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Release files / kcounter-0.1.2-cp314-cp314-macosx_10_12_x86_64.whl
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twine/6.2.0 CPython/3.13.9
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Release files / kcounter-0.1.2-cp313-cp313t-musllinux_1_2_x86_64.whl
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twine/6.2.0 CPython/3.13.9
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Release files / kcounter-0.1.2-cp313-cp313t-musllinux_1_2_i686.whl
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twine/6.2.0 CPython/3.13.9
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Release files / kcounter-0.1.2-cp313-cp313t-musllinux_1_2_armv7l.whl
| Download URL | kcounter-0.1.2-cp313-cp313t-musllinux_1_2_armv7l.whl |
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| Size | 538.5 kB |
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twine/6.2.0 CPython/3.13.9
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Release files / kcounter-0.1.2-cp313-cp313t-musllinux_1_2_aarch64.whl
| Download URL | kcounter-0.1.2-cp313-cp313t-musllinux_1_2_aarch64.whl |
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| Size | 432.7 kB |
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twine/6.2.0 CPython/3.13.9
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Release files / kcounter-0.1.2-cp313-cp313t-manylinux_2_17_armv7l.manylinux2014_armv7l.whl
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twine/6.2.0 CPython/3.13.9
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Release files / kcounter-0.1.2-cp313-cp313t-manylinux_2_17_aarch64.manylinux2014_aarch64.whl
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| Size | 256.0 kB |
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No |
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twine/6.2.0 CPython/3.13.9
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Release files / kcounter-0.1.2-cp313-cp313-win_amd64.whl
| Download URL | kcounter-0.1.2-cp313-cp313-win_amd64.whl |
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| Size | 170.9 kB |
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No |
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twine/6.2.0 CPython/3.13.9
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Release files / kcounter-0.1.2-cp313-cp313-musllinux_1_2_x86_64.whl
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twine/6.2.0 CPython/3.13.9
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Release files / kcounter-0.1.2-cp313-cp313-musllinux_1_2_i686.whl
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| Size | 497.2 kB |
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Release files / kcounter-0.1.2-cp313-cp313-musllinux_1_2_armv7l.whl
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| Size | 538.7 kB |
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No |
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twine/6.2.0 CPython/3.13.9
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Release files / kcounter-0.1.2-cp313-cp313-musllinux_1_2_aarch64.whl
| Download URL | kcounter-0.1.2-cp313-cp313-musllinux_1_2_aarch64.whl |
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| Size | 431.8 kB |
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No |
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twine/6.2.0 CPython/3.13.9
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Release files / kcounter-0.1.2-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
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| Size | 259.6 kB |
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No |
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twine/6.2.0 CPython/3.13.9
|
Release files / kcounter-0.1.2-cp313-cp313-manylinux_2_17_armv7l.manylinux2014_armv7l.whl
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No |
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twine/6.2.0 CPython/3.13.9
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Release files / kcounter-0.1.2-cp313-cp313-manylinux_2_17_aarch64.manylinux2014_aarch64.whl
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| Size | 255.4 kB |
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No |
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twine/6.2.0 CPython/3.13.9
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Release files / kcounter-0.1.2-cp313-cp313-manylinux_2_5_i686.manylinux1_i686.whl
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No |
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twine/6.2.0 CPython/3.13.9
|
Release files / kcounter-0.1.2-cp313-cp313-macosx_11_0_arm64.whl
| Download URL | kcounter-0.1.2-cp313-cp313-macosx_11_0_arm64.whl |
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| Size | 223.4 kB |
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No |
| Uploaded via |
twine/6.2.0 CPython/3.13.9
|
Release files / kcounter-0.1.2-cp313-cp313-macosx_10_12_x86_64.whl
| Download URL | kcounter-0.1.2-cp313-cp313-macosx_10_12_x86_64.whl |
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No |
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twine/6.2.0 CPython/3.13.9
|
Release files / kcounter-0.1.2-cp312-cp312-win_amd64.whl
| Download URL | kcounter-0.1.2-cp312-cp312-win_amd64.whl |
|---|---|
| Size | 171.4 kB |
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No |
| Uploaded via |
twine/6.2.0 CPython/3.13.9
|
Release files / kcounter-0.1.2-cp312-cp312-musllinux_1_2_x86_64.whl
| Download URL | kcounter-0.1.2-cp312-cp312-musllinux_1_2_x86_64.whl |
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| Size | 462.3 kB |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.2.0 CPython/3.13.9
|
Release files / kcounter-0.1.2-cp312-cp312-musllinux_1_2_i686.whl
| Download URL | kcounter-0.1.2-cp312-cp312-musllinux_1_2_i686.whl |
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| Size | 497.7 kB |
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No |
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twine/6.2.0 CPython/3.13.9
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Release files / kcounter-0.1.2-cp312-cp312-musllinux_1_2_armv7l.whl
| Download URL | kcounter-0.1.2-cp312-cp312-musllinux_1_2_armv7l.whl |
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| Size | 539.2 kB |
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No |
| Uploaded via |
twine/6.2.0 CPython/3.13.9
|
Release files / kcounter-0.1.2-cp312-cp312-musllinux_1_2_aarch64.whl
| Download URL | kcounter-0.1.2-cp312-cp312-musllinux_1_2_aarch64.whl |
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| Size | 431.9 kB |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
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twine/6.2.0 CPython/3.13.9
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Release files / kcounter-0.1.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | kcounter-0.1.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
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| Size | 260.1 kB |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.2.0 CPython/3.13.9
|
Release files / kcounter-0.1.2-cp312-cp312-manylinux_2_17_armv7l.manylinux2014_armv7l.whl
| Download URL | kcounter-0.1.2-cp312-cp312-manylinux_2_17_armv7l.manylinux2014_armv7l.whl |
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| Size | 264.1 kB |
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No |
| Uploaded via |
twine/6.2.0 CPython/3.13.9
|
Release files / kcounter-0.1.2-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl
| Download URL | kcounter-0.1.2-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl |
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| Size | 255.5 kB |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
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twine/6.2.0 CPython/3.13.9
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Release files / kcounter-0.1.2-cp312-cp312-manylinux_2_5_i686.manylinux1_i686.whl
| Download URL | kcounter-0.1.2-cp312-cp312-manylinux_2_5_i686.manylinux1_i686.whl |
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| Size | 276.6 kB |
| Tags | CPython 3.12 Linux glibc 2.5+ x86-32 |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.2.0 CPython/3.13.9
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Release files / kcounter-0.1.2-cp312-cp312-macosx_11_0_arm64.whl
| Download URL | kcounter-0.1.2-cp312-cp312-macosx_11_0_arm64.whl |
|---|---|
| Size | 223.5 kB |
| Tags | CPython 3.12 macOS 11.0+ ARM64 |
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SHA-256 checksum How to use checksums |
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No |
| Uploaded via |
twine/6.2.0 CPython/3.13.9
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Release files / kcounter-0.1.2-cp312-cp312-macosx_10_12_x86_64.whl
| Download URL | kcounter-0.1.2-cp312-cp312-macosx_10_12_x86_64.whl |
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| Size | 224.5 kB |
| Tags | CPython 3.12 macOS 10.12+ x86-64 |
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No |
| Uploaded via |
twine/6.2.0 CPython/3.13.9
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Security for kcounter 0.1.2
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