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
5pUTR: UTR reporting
validateFormat: Check that the file conforms with the BED format
Installing is as simple as:
pip install bedparse
The basic syntax in the form:
bedparse subcommand [parameters].
For a list of all subcommands and a brief explanation of what they do, use:
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
Our documentation is hosted on Read the Docs.
We also have a short tutorial to guide you through the basic functions.
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