Metadata-Version: 2.1
Name: bedparse
Version: 0.2.2
Summary: A simple library and CLI tool to manipulate BED files
Home-page: https://github.com/tleonardi/bedparse
Author: Tommaso Leonardi
Author-email: tom@tleo.io
License: MIT
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3.2
Classifier: Programming Language :: Python :: 3.3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Requires-Python: >=3
Description-Content-Type: text/markdown
Requires-Dist: argparse
Requires-Dist: setuptools

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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.



