Bedparse

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.

We also have a short tutorial to guide you through the basic functions.

Publications

If you use bedparse please cite the following paper:

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