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 annotationsjoin: Joining of annotation files based on transcript namesgtf2bed: Conversion from GTF to BED formatconvertChr: Conversion from UCSC to Ensembl chromosome names (and viceversa)bed12tobed6: Conversion from bed12 to bed6promoter: Promoter reportingintrons: Intron reportingcds: CDS reporting3pUTRand5pUTR: UTR reportingvalidateFormat: 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: 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
Our documentation is hosted on Read the Docs.
We also have a short tutorial to guide you through the basic functions.