<commit_before>Uncle PSL: a BLAT to SAM converter
==================================


Installation
------------

Install the package:

```
python setup.py install
```

Install the package in developer mode:

```
python setup.py develop
```

Run the tests:

```
make test
```

Build the documentation:

```
make docs
```

Issue `make help` to get a list of `make` targets.

Documentation
-------------

Documentation can be found at: https://bsipos.git.oxfordnanolabs.local/uncle_PSL

Contributing
------------

- Please fork the repository and create a merge request to contribute.
- Please respect the structure outlined in `scripts/_template_script.py` from command line tools so documentation can be generated automatically.
- Use [bumpversion](http://bit.ly/2cSUryt) to manage package versioning.
- The code should be [PEP8](https://www.python.org/dev/peps/pep-0008) compliant, which can be tested by `make lint`.
- For more guidance regarding coding style please refer to the [Tao of Tang](https://git.oxfordnanolabs.local/research/tang/blob/master/tao.md).

TODO
----<commit_msg>README update.<commit_after>Uncle PSL: a BLAT to SAM converter
==================================


Installation
------------

Install the package:

```
python setup.py install
```

Install the package in developer mode:

```
python setup.py develop
```

Run the tests:

```
make test
```

Build the documentation:

```
make docs
```

Issue `make help` to get a list of `make` targets.

Documentation
-------------

Documentation can be found at: https://bsipos.git.oxfordnanolabs.local/uncle_psl

Contributing
------------

- Please fork the repository and create a merge request to contribute.
- Please respect the structure outlined in `scripts/_template_script.py` from command line tools so documentation can be generated automatically.
- Use [bumpversion](http://bit.ly/2cSUryt) to manage package versioning.
- The code should be [PEP8](https://www.python.org/dev/peps/pep-0008) compliant, which can be tested by `make lint`.
- For more guidance regarding coding style please refer to the [Tao of Tang](https://git.oxfordnanolabs.local/research/tang/blob/master/tao.md).

TODO
----
{'fraction_non_alphanumeric': 0.16244822825586747, 'fraction_numerical': 0.005522319374137137, 'mean_word_length': 3.715835140997831, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 6, 'lorem ipsum': 0, 'www.': 2, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '4240300', 'n_tokens_mistral': 669, 'n_tokens_neox': 622, 'n_words': 225}