# hkgfinder
[](https://pypi.org/project/hkgfinder)
[](https://pypi.org/project/hkgfinder)
[](https://pypi.org/project/hkgfinder)
[](https://pypi.org/project/hkgfinder)
[](https://pypi.org/project/hkgfinder)
[](https://www.gnu.org/licenses/MIT)
## Find housekeeping genes in prokaryotic (meta)genomes
### Introduction
hkgfinder is a fast and accurate housekeeping gene finder and classifier. hkgfinder can run on raw sequences, genomes and metagenomes. The novel value of this method lies is in its ability to directly predict and classify gene sequences into housekeeping gene families at a high specificity and sensitivity, while being also faster than genome and metagenome annotator on genome and metagenome data.
### How hkgfinder works
### Installation
~~You will have first to install [Prodigal](https://github.com/hyattpd/Prodigal) and [HMMER 3](https://hmmer.org) to be able to run hkgfinder.~~
**hkgfinder since v0.2 is without external dependencies.**
```bash
pip install hkgfinder
```
## Test
* Type `hkgfinder -h` and it should output something like:
```
usage: hkgfinder [options] [<FILE>]
options:
-o [FILE] output result to FILE [stdout]
-g activate genome mode [false]
-m activate metagenome mode [false]
--faa FILE output matched protein sequences to FILE [false]
--fna FILE output matched DNA sequences to FILE [false]
-s output sequences in file by gene [false]
-t INT number of threads [1]
-q decrease program verbosity
-d enable debug mode
-v, --version show program's version number and exit
-h, --help show this help message and exit
```
## Invoking hkgfinder
```
hkgfinder --faa housekeeping.faa --fna housekeeping.fna file.fa.gz
```
* hkgfinder supports gzip, lzma, bz2 and zstd compressed files.
## Bugs
Submit problems or requests to the [Issue Tracker](https://github.com/Ebedthan/hkgfinder/issues).
## Licence
[MIT](https://github.com/Ebedthan/hkgfinder/blob/main/LICENSE).
## Author
* [Anicet Ebou](https://orcid.org/0000-0003-4005-177X)
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