bedspec 0.2.0__tar.gz

bedspec-0.2.0/CONTRIBUTING.md

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+# Development and Testing
+
+## Local Installation
+
+First install the Python packaging and dependency management tool [`poetry`](https://python-poetry.org/docs/#installation).
+You must have Python 3.12 or greater available on your system path, which could be managed by [`pyenv`](https://github.com/pyenv/pyenv) or another package manager. 
+Finally, install the dependencies of the project with:
+
+```console
+poetry install
+```
+
+## Running Tests
+
+To test the codebase, run the following command:
+
+```console
+poetry run pytest
+```
+
+The command will:
+
+- Execute unit tests with [`pytest`](https://docs.pytest.org/)
+- Test the language typing with [`mypy`](https://mypy-lang.org/)
+- Test for linting and styling errors with [`ruff`](https://docs.astral.sh/ruff/)
+- Emit a testing coverage report with [`coverage`](https://coverage.readthedocs.io/)
+
+To format the code in the library, run the following commands:
+
+```console
+poetry run ruff check --select I --fix
+poetry run ruff format bedspec tests
+```
+
+To generate a code coverage report locally, run the following command:
+
+```console
+poetry run coverage html
+```

bedspec-0.2.0/LICENSE

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+MIT License
+
+Copyright © 2024 Clint Valentine
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

bedspec-0.2.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: bedspec
+Version: 0.2.0
+Summary: An HTS-specs compliant BED toolkit.
+Home-page: https://github.com/clintval/bedspec
+License: MIT
+Keywords: bioinformatics
+Author: Clint Valentine
+Author-email: valentine.clint@gmail.com
+Requires-Python: >=3.12,<4.0
+Classifier: Development Status :: 3 - Alpha
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Software Development :: Documentation
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Project-URL: Repository, https://github.com/clintval/bedspec
+Description-Content-Type: text/markdown
+
+# bedspec
+
+[![PyPi Release](https://badge.fury.io/py/bedspec.svg)](https://badge.fury.io/py/bedspec)
+[![CI](https://github.com/clintval/bedspec/actions/workflows/tests.yml/badge.svg?branch=main)](https://github.com/clintval/bedspec/actions/workflows/tests.yml?query=branch%3Amain)
+[![Python Versions](https://img.shields.io/badge/python-3.12-blue)](https://github.com/clintval/bedspec)
+[![MyPy Checked](http://www.mypy-lang.org/static/mypy_badge.svg)](http://mypy-lang.org/)
+[![Poetry](https://img.shields.io/endpoint?url=https://python-poetry.org/badge/v0.json)](https://python-poetry.org/)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://docs.astral.sh/ruff/)
+
+An HTS-specs compliant BED toolkit.
+
+## Installation
+
+The package can be installed with `pip`:
+
+```console
+pip install bedspec
+```
+
+## Quickstart
+
+### Writing
+
+```python
+from bedspec import BedWriter, Bed3
+
+bed = Bed3("chr1", start=2, end=8)
+
+with BedWriter(open("test.bed", "w")) as writer:
+    writer.write(bed)
+```
+
+### Reading
+
+```python
+from bedspec import BedReader, Bed3
+
+with BedReader[Bed3](open("test.bed")) as reader:
+    for bed in reader:
+        print(bed)
+```
+```console
+Bed3(contig="chr1", start=2, start=8)
+```
+
+### BED Types
+
+This package provides pre-defined classes for the following BED formats:
+
+```python
+from bedspec import Bed2
+from bedspec import Bed3
+from bedspec import Bed4
+from bedspec import Bed5
+from bedspec import Bed6
+from bedspec import BedPE
+```
+
+### Custom BED Types
+
+To create a custom BED record, inherit from the relevent BED-type:
+
+| Type        | Description                                          |
+| ---         | ---                                                  |
+| `PointBed`  | BED records that are a single point (1-length) only. |
+| `SimpleBed` | BED records that are a single interval.              |
+| `PairBed`   | BED records that are a pair of intervals.            |
+
+For example, to create a custom BED3+1 class:
+
+```python
+from dataclasses import dataclass
+
+from bedspec import SimpleBed
+
+@dataclass
+class MyCustomBed(SimpleBed):
+    contig: str
+    start: int
+    end: int
+    my_custom_field: float
+```
+
+## Development and Testing
+
+See the [contributing guide](./CONTRIBUTING.md) for more information.
+

bedspec-0.2.0/README.md

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+# bedspec
+
+[![PyPi Release](https://badge.fury.io/py/bedspec.svg)](https://badge.fury.io/py/bedspec)
+[![CI](https://github.com/clintval/bedspec/actions/workflows/tests.yml/badge.svg?branch=main)](https://github.com/clintval/bedspec/actions/workflows/tests.yml?query=branch%3Amain)
+[![Python Versions](https://img.shields.io/badge/python-3.12-blue)](https://github.com/clintval/bedspec)
+[![MyPy Checked](http://www.mypy-lang.org/static/mypy_badge.svg)](http://mypy-lang.org/)
+[![Poetry](https://img.shields.io/endpoint?url=https://python-poetry.org/badge/v0.json)](https://python-poetry.org/)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://docs.astral.sh/ruff/)
+
+An HTS-specs compliant BED toolkit.
+
+## Installation
+
+The package can be installed with `pip`:
+
+```console
+pip install bedspec
+```
+
+## Quickstart
+
+### Writing
+
+```python
+from bedspec import BedWriter, Bed3
+
+bed = Bed3("chr1", start=2, end=8)
+
+with BedWriter(open("test.bed", "w")) as writer:
+    writer.write(bed)
+```
+
+### Reading
+
+```python
+from bedspec import BedReader, Bed3
+
+with BedReader[Bed3](open("test.bed")) as reader:
+    for bed in reader:
+        print(bed)
+```
+```console
+Bed3(contig="chr1", start=2, start=8)
+```
+
+### BED Types
+
+This package provides pre-defined classes for the following BED formats:
+
+```python
+from bedspec import Bed2
+from bedspec import Bed3
+from bedspec import Bed4
+from bedspec import Bed5
+from bedspec import Bed6
+from bedspec import BedPE
+```
+
+### Custom BED Types
+
+To create a custom BED record, inherit from the relevent BED-type:
+
+| Type        | Description                                          |
+| ---         | ---                                                  |
+| `PointBed`  | BED records that are a single point (1-length) only. |
+| `SimpleBed` | BED records that are a single interval.              |
+| `PairBed`   | BED records that are a pair of intervals.            |
+
+For example, to create a custom BED3+1 class:
+
+```python
+from dataclasses import dataclass
+
+from bedspec import SimpleBed
+
+@dataclass
+class MyCustomBed(SimpleBed):
+    contig: str
+    start: int
+    end: int
+    my_custom_field: float
+```
+
+## Development and Testing
+
+See the [contributing guide](./CONTRIBUTING.md) for more information.

bedspec-0.2.0/bedspec/__init__.py

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+# ruff: noqa: F401
+from ._bedspec import COMMENT_PREFIXES
+from ._bedspec import MISSING_FIELD
+from ._bedspec import Bed2
+from ._bedspec import Bed3
+from ._bedspec import Bed4
+from ._bedspec import Bed5
+from ._bedspec import Bed6
+from ._bedspec import BedColor
+from ._bedspec import BedPE
+from ._bedspec import BedReader
+from ._bedspec import BedStrand
+from ._bedspec import BedType
+from ._bedspec import BedWriter
+from ._bedspec import PairBed
+from ._bedspec import PointBed
+from ._bedspec import SimpleBed
+from ._bedspec import Stranded