semvec/pypi-packages huggingface dataset:
bedparse 0.2.3
A simple library and CLI tool to manipulate BED files
License: MIT
Requires Python: >=3.4

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# Bedparse

![](docs/bedparse.svg)

Bedparse is a simple python module and CLI tool to perform common operations on BED files.

It offers 11 sub-commands that implement the following functionality:
* `filter`: Filtering of transcripts based on annotations
* `join`: Joining of annotation files based on transcript names
* `gtf2bed`: Conversion from GTF to BED format
* `convertChr`: Conversion from UCSC to Ensembl chromosome names (and viceversa)
* `bed12tobed6`: Conversion from bed12 to bed6
* `promoter`: Promoter reporting
* `introns`: Intron reporting
* `cds`: CDS reporting
* `3pUTR` and `5pUTR`: UTR reporting 
* `validateFormat`: Check that the file conforms with the BED format

## Installation

Installing is as simple as:

```
pip install bedparse
```

## Basic usage

The basic syntax in the form: `bedparse subcommand [parameters]`.

For a list of all subcommands and a brief explanation of what they do, use: `bedparse --help`.

For a detailed explanation of each subcommand and a list of its parameters, use the `--help` option after the subcommand's name, e.g.: `bedparse promoter --help`

## Documentation

Our documentation is hosted on [Read the Docs](https://bedparse.readthedocs.io/en/latest/).

We also have a short [tutorial](https://bedparse.readthedocs.io/en/latest/Tutorial.html) to guide you through the basic functions.


## Publications

If you use bedparse please cite the following [paper](https://joss.theoj.org/papers/10.21105/joss.01228):

_Leonardi, (2019). Bedparse: feature extraction from BED files. Journal of Open Source Software, 4(34), 1228, https://doi.org/10.21105/joss.01228_