BED File Annotator

This script annotates a BED file with gene information using the Ensembl REST API. It is specifically designed to work with human genome build GRCh37 (hg19).

Prerequisites

• Python 3.7 or higher
• pandas
• requests

You can install the required Python packages using pip:

pip install pandas requests

Usage

Clone the repository:

git clone https://github.com/vsmicrogenomics/bed-annotator.git cd bed-annotator

Place your BED file (e.g., Probe.bed) in the same directory as the script.

Run the script: python bed-annotator.py

The annotated BED file (Annotated_Probe.bed) will be generated in the same directory.

Example Input BED file (Probe.bed): chr1 10292379 10292499 chr1 10308880 10309000 chr1 10316282 10316402

Output Annotated BED file (Annotated_Probe.bed): chrom start end gene_start gene_end gene_name chr1 10292379 10292499 10270863.0 10441661.0 KIF1B chr1 10308880 10309000 10270863.0 10441661.0 KIF1B chr1 10316282 10316402 10270863.0 10441661.0 KIF1B

Script Details

The script reads a BED file, queries the Ensembl REST API for gene information, and writes the annotations back to a new BED file. The following information is added to each region in the BED file:

Gene start position Gene end position Gene name

Acknowledgments

This script uses the Ensembl REST API to retrieve gene annotations. We thank the Ensembl team for providing this valuable resource.

Citation

If you use this script for your research, please consider citing it as follows: Sharma, V. (2024). bed-annotator.py [Python script]. Retrieved from https://github.com/vsmicrogenomics/bed-annotator