# bedspec
[](https://badge.fury.io/py/bedspec)
[](https://github.com/clintval/bedspec/actions/workflows/tests.yml?query=branch%3Amain)
[](https://github.com/clintval/bedspec)
[](http://mypy-lang.org/)
[](https://python-poetry.org/)
[](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.
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