semvec/pypi-packages huggingface dataset:
hkgfinder 0.3.0
find housekeeping genes in prokaryotic (meta)genomic data
License: MIT
Requires Python: <4.0,>=3.8
Keywords: bioinformatics

# hkgfinder

*Find housekeeping genes in prokaryotic (meta)genomes*

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## 🗺️ Overview
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
![](img/hkgfinder.png)

## 🔧 Installing

hkgfinder can be installed directly from [PyPI](https://pypi.org/project/hkgfinder).

```console
$ 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.
  
## ⚠️ Issue Tracker

Found a bug ? Have an enhancement request ? Head over to the [Issue Tracker](https://github.com/Ebedthan/hkgfinder/issues) if you need to report
or ask something. If you are filing in on a bug, please include as much
information as you can about the issue, and try to recreate the same bug
in a simple, easily reproducible situation.


## ⚖️ License

[MIT](https://github.com/Ebedthan/hkgfinder/blob/main/LICENSE).


## Author

* [Anicet Ebou](https://orcid.org/0000-0003-4005-177X)
pickle-tool 0.1.0
基于pickle的拓展工具
License: MIT

============
pickle工具
============

============
1.如何安装
============

::

    pip install pickle_tool

========================
2.该包包含的方法
========================
------------------------
save_to_pickle
------------------------
装饰器，若被装饰的函数有返回值，在该函数外层加上该装饰器，则会将函数的返回对象序列化保存到磁盘，下次调用该函数时直接读磁盘的序列化结果
用于节省一些耗时的运算结果保存在本地，以免下次要重复计算

示例：
::

    @save_to_pickle("tmp.pickle", overwrite=False)
    def foo():
        return 1

则当下次再运行该函数，会直接读取"tmp.pickle"文件，并返回保存的结果

------------------------
load_pickle
------------------------
简化了对pickle的读取操作，不需要再额外使用open()来打开文件

::

    obj = load_pickle("tmp.pickle")