Bedparse: feature extraction from BED files
Tommaso Leonardi · The Journal of Open Source Software · 2019
Bedparse is a Python module and command-line interface tool to extract features from genome annotation files in BED (Browser Extensible Data) format.The BED format is a plaintext file format commonly used in bioinformatics to represent genomic features.Each line in a BED file corresponds to a genomic feature (e.g. a gene, transcript, peak, regulatory region, etc.) and consists of up to 12 tab-separated fields that define its genomic coordinates and exon-intron structure.This format is also commonly used to graphically visualise genomic features by genome browser software and is one of the standard formats used by the UCSC (Kent et al., 2002) and Ensembl (Zerbino et al., 2018) genome browsers.One of the major advantages of the BED format over many of its alternatives is that each line includes all the information required to define an individual gene/transcript model.This makes the format particulary convenient when used with Unix pipes, awk one-liners or small custom scripts.This ad hoc approach, albeit (usually) simple and effective, often leads to repetition and/or code duplication and can be prone to errors, bugs and typos that are not always easy to detect.