<filename>pafpy/__init__.py
"""A lightweight library for working with [PAF][PAF] (Pairwise mApping Format) files.

[![GitHub Workflow Status](https://img.shields.io/github/workflow/status/mbhall88/pafpy/Python_package)](https://github.com/mbhall88/pafpy/actions)
[![codecov](https://codecov.io/gh/mbhall88/pafpy/branch/master/graph/badge.svg)](https://codecov.io/gh/mbhall88/pafpy)
[![PyPI](https://img.shields.io/pypi/v/pafpy)](https://pypi.org/project/pafpy/)
![PyPI - Python Version](https://img.shields.io/pypi/pyversions/pafpy)
![License](https://img.shields.io/github/license/mbhall88/pafpy)
[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)


# Install

### PyPi

```sh
pip install pafpy
```

### Conda

```sh
conda install -c bioconda pafpy
```

### Locally

If you would like to install locally, the recommended way is using [poetry][poetry].

```sh
git clone https://github.com/mbhall88/pafpy.git
cd pafpy
make install
# to check the library is installed run
poetry run python -c "from pafpy import PafRecord;print(str(PafRecord()))"
# you should see a (unmapped) PAF record printed to the terminal
# you can also run the tests if you like
make test-code
```

.. include:: ../docs/USAGE.md

[poetry]: https://python-poetry.org/
[PAF]: https://github.com/lh3/miniasm/blob/master/PAF.md
[docs]: https://pafpy.xyz
[blast]: https://lh3.github.io/2018/11/25/on-the-definition-of-sequence-identity#blast-identity
[contribute]: https://github.com/mbhall88/pafpy/blob/master/CONTRIBUTING.md

.. include:: ../CONTRIBUTING.md
"""
from pafpy.__version__ import __version__  # noqa: F401
from pafpy.paffile import PafFile  # noqa: F401
from pafpy.pafrecord import AlignmentType, MalformattedRecord, PafRecord  # noqa: F401
from pafpy.strand import Strand  # noqa: F401
from pafpy.tag import InvalidTagFormat, Tag, TagType, UnknownTagTypeChar  # noqa: F401

<filename>pafpy/__init__.py
"""A lightweight library for working with [PAF][PAF] (Pairwise mApping Format) files.

[![GitHub Workflow Status](https://img.shields.io/github/workflow/status/mbhall88/pafpy/Python_package)](https://github.com/mbhall88/pafpy/actions)
[![codecov](https://codecov.io/gh/mbhall88/pafpy/branch/master/graph/badge.svg)](https://codecov.io/gh/mbhall88/pafpy)
[![PyPI](https://img.shields.io/pypi/v/pafpy)](https://pypi.org/project/pafpy/)
![PyPI - Python Version](https://img.shields.io/pypi/pyversions/pafpy)
![License](https://img.shields.io/github/license/mbhall88/pafpy)
[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)


# Install

### PyPi

```sh
pip install pafpy
```

### Conda

```sh
conda install -c bioconda pafpy
```

### Locally

If you would like to install locally, the recommended way is using [poetry][poetry].

```sh
git clone https://github.com/mbhall88/pafpy.git
cd pafpy
make install
# to check the library is installed run
poetry run python -c "from pafpy import PafRecord;print(str(PafRecord()))"
# you should see a (unmapped) PAF record printed to the terminal
# you can also run the tests if you like
make test-code
```

.. include:: ../docs/USAGE.md

[poetry]: https://python-poetry.org/
[PAF]: https://github.com/lh3/miniasm/blob/master/PAF.md
[docs]: https://pafpy.xyz
[blast]: https://lh3.github.io/2018/11/25/on-the-definition-of-sequence-identity#blast-identity
[contribute]: https://github.com/mbhall88/pafpy/blob/master/CONTRIBUTING.md

.. include:: ../CONTRIBUTING.md
"""
from pafpy.__version__ import __version__  # noqa: F401
from pafpy.paffile import PafFile  # noqa: F401
from pafpy.pafrecord import AlignmentType, MalformattedRecord, PafRecord  # noqa: F401
from pafpy.strand import Strand  # noqa: F401
from pafpy.tag import InvalidTagFormat, Tag, TagType, UnknownTagTypeChar  # noqa: F401

A lightweight library for working with [PAF][PAF] (Pairwise mApping Format) files.  [![GitHub Workflow Status](https://img.shields.io/github/workflow/status/mbhall88/pafpy/Python_package)](https://github.com/mbhall88/pafpy/actions) [![codecov](https://codecov.io/gh/mbhall88/pafpy/branch/master/graph/badge.svg)](https://codecov.io/gh/mbhall88/pafpy) [![PyPI](https://img.shields.io/pypi/v/pafpy)](https://pypi.org/project/pafpy/) ![PyPI - Python Version](https://img.shields.io/pypi/pyversions/pafpy) ![License](https://img.shields.io/github/license/mbhall88/pafpy) [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)   # Install  ### PyPi  ```sh pip install pafpy ```  ### Conda  ```sh conda install -c bioconda pafpy ```  ### Locally  If you would like to install locally, the recommended way is using [poetry][poetry].  ```sh git clone https://github.com/mbhall88/pafpy.git cd pafpy make install # to check the library is installed run poetry run python -c "from pafpy import PafRecord;print(str(PafRecord()))" # you should see a (unmapped) PAF record printed to the terminal # you can also run the tests if you like make test-code ```  .. include:: ../docs/USAGE.md  [poetry]: https://python-poetry.org/ [PAF]: https://github.com/lh3/miniasm/blob/master/PAF.md [docs]: https://pafpy.xyz [blast]: https://lh3.github.io/2018/11/25/on-the-definition-of-sequence-identity#blast-identity [contribute]: https://github.com/mbhall88/pafpy/blob/master/CONTRIBUTING.md  .. include:: ../CONTRIBUTING.md # noqa: F401 # noqa: F401 # noqa: F401 # noqa: F401 # noqa: F401