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
and5pUTR
: 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