https://github.com/tleonardi/bedparse

Python module and CLI tool to perform operations on BED files
https://github.com/tleonardi/bedparse

bed-files bioinformatics cli

Last synced: about 1 year ago
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Python module and CLI tool to perform operations on BED files

• Host: GitHub
• URL: https://github.com/tleonardi/bedparse
• Owner: tleonardi
• License: mit
• Created: 2017-06-09T08:44:25.000Z (about 9 years ago)
• Default Branch: master
• Last Pushed: 2020-01-23T12:04:55.000Z (over 6 years ago)
• Last Synced: 2025-04-11T12:07:22.620Z (about 1 year ago)
• Topics: bed-files, bioinformatics, cli
• Language: Python
• Homepage: http://bedparse.rtfd.io
• Size: 67.4 MB
• Stars: 12
• Watchers: 3
• Forks: 4
• Open Issues: 4
• Metadata Files:
  • Readme: README.md
  • Changelog: Changelog.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE.txt

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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_