# bedspec
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[](https://github.com/clintval/bedspec/actions/workflows/tests.yml?query=branch%3Amain)
[](https://github.com/clintval/typeline)
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An HTS-specs compliant BED toolkit.
## Installation
The package can be installed with `pip`:
```console
pip install bedspec
```
## Quickstart
### Building a BED Feature
```pycon
>>> from bedspec import Bed3
>>>
>>> bed = Bed3("chr1", start=2, end=8)
```
### Writing
```pycon
>>> from bedspec import BedWriter
>>> from tempfile import NamedTemporaryFile
>>>
>>> temp_file = NamedTemporaryFile(mode="w+t", suffix=".txt")
>>>
>>> with BedWriter.from_path(temp_file.name, Bed3) as writer:
... writer.write(bed)
```
### Reading
```pycon
>>> from bedspec import BedReader
>>>
>>> with BedReader.from_path(temp_file.name, Bed3) as reader:
... for bed in reader:
... print(bed)
Bed3(refname='chr1', start=2, end=8)
```
### BED Types
This package provides builtin classes for the following BED formats:
```pycon
>>> from bedspec import Bed2
>>> from bedspec import Bed3
>>> from bedspec import Bed4
>>> from bedspec import Bed5
>>> from bedspec import Bed6
>>> from bedspec import Bed12
>>> from bedspec import BedGraph
>>> from bedspec import BedPE
```
### Overlap Detection
Use a fast overlap detector for any collection of interval types, including third-party:
```pycon
>>> from bedspec import Bed3, Bed4
>>> from bedspec.overlap import OverlapDetector
>>>
>>> bed1 = Bed3("chr1", start=1, end=4)
>>> bed2 = Bed3("chr1", start=5, end=9)
>>>
>>> detector = OverlapDetector[Bed3]([bed1, bed2])
>>>
>>> my_feature = Bed4("chr1", start=2, end=3, name="hi-mom")
>>> detector.overlaps(my_feature)
True
```
The overlap detector supports the following operations:
- `overlapping`: return all overlapping features
- `overlaps`: test if any overlapping features exist
- `enclosed_by`: return those enclosed by the input feature
- `enclosing`: return those enclosing the input feature
### Custom BED Types
To create a custom BED record, inherit from the relevant BED-type (`PointBed`, `SimpleBed`, `PairBed`).
For example, to create a custom BED3+1 class:
```pycon
>>> from dataclasses import dataclass
>>>
>>> from bedspec import SimpleBed
>>>
>>> @dataclass(eq=True)
... class Bed3Plus1(SimpleBed):
... refname: str
... start: int
... end: int
... my_custom_field: float | None
```
## Development and Testing
See the [contributing guide](./CONTRIBUTING.md) for more information.
Raw data
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"description": "# bedspec\n\n[](https://badge.fury.io/py/bedspec)\n[](https://github.com/clintval/bedspec/actions/workflows/tests.yml?query=branch%3Amain)\n[](https://github.com/clintval/typeline)\n[](https://docs.basedpyright.com/latest/)\n[](https://mypy-lang.org/)\n[](https://python-poetry.org/)\n[](https://docs.astral.sh/ruff/)\n\nAn HTS-specs compliant BED toolkit.\n\n## Installation\n\nThe package can be installed with `pip`:\n\n```console\npip install bedspec\n```\n\n## Quickstart\n\n### Building a BED Feature\n\n```pycon\n>>> from bedspec import Bed3\n>>> \n>>> bed = Bed3(\"chr1\", start=2, end=8)\n\n```\n\n### Writing\n\n```pycon\n>>> from bedspec import BedWriter\n>>> from tempfile import NamedTemporaryFile\n>>> \n>>> temp_file = NamedTemporaryFile(mode=\"w+t\", suffix=\".txt\")\n>>>\n>>> with BedWriter.from_path(temp_file.name, Bed3) as writer:\n... writer.write(bed)\n\n```\n\n### Reading\n\n```pycon\n>>> from bedspec import BedReader\n>>> \n>>> with BedReader.from_path(temp_file.name, Bed3) as reader:\n... for bed in reader:\n... print(bed)\nBed3(refname='chr1', start=2, end=8)\n\n```\n\n### BED Types\n\nThis package provides builtin classes for the following BED formats:\n\n```pycon\n>>> from bedspec import Bed2\n>>> from bedspec import Bed3\n>>> from bedspec import Bed4\n>>> from bedspec import Bed5\n>>> from bedspec import Bed6\n>>> from bedspec import Bed12\n>>> from bedspec import BedGraph\n>>> from bedspec import BedPE\n\n```\n\n### Overlap Detection\n\nUse a fast overlap detector for any collection of interval types, including third-party:\n\n```pycon\n>>> from bedspec import Bed3, Bed4\n>>> from bedspec.overlap import OverlapDetector\n>>>\n>>> bed1 = Bed3(\"chr1\", start=1, end=4)\n>>> bed2 = Bed3(\"chr1\", start=5, end=9)\n>>> \n>>> detector = OverlapDetector[Bed3]([bed1, bed2])\n>>> \n>>> my_feature = Bed4(\"chr1\", start=2, end=3, name=\"hi-mom\")\n>>> detector.overlaps(my_feature)\nTrue\n\n```\n\nThe overlap detector supports the following operations:\n\n- `overlapping`: return all overlapping features\n- `overlaps`: test if any overlapping features exist\n- `enclosed_by`: return those enclosed by the input feature\n- `enclosing`: return those enclosing the input feature\n\n### Custom BED Types\n\nTo create a custom BED record, inherit from the relevant BED-type (`PointBed`, `SimpleBed`, `PairBed`).\n\nFor example, to create a custom BED3+1 class:\n\n```pycon\n>>> from dataclasses import dataclass\n>>> \n>>> from bedspec import SimpleBed\n>>> \n>>> @dataclass(eq=True)\n... class Bed3Plus1(SimpleBed):\n... refname: str\n... start: int\n... end: int\n... my_custom_field: float | None\n\n```\n\n## Development and Testing\n\nSee the [contributing guide](./CONTRIBUTING.md) for more information.\n\n",
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