{"repo":"wheretrue/biobear","free":true,"listed":false,"github":"https://github.com/wheretrue/biobear","clone":"git clone https://github.com/wheretrue/biobear.git","description":"Work with bioinformatic files using Arrow, Polars, and/or DuckDB","language":"Rust","stars":196,"topics":["bioinformatics","biology","rust-bio","samtools","arrow","python","biopython","duckdb","polars","pyarrow"],"license":"MIT","category":"data-pipelines","readme_excerpt":"biobear is a Python library designed for reading and searching bioinformatic file formats, using Rust as its backend and producing Arrow Batch Readers and other downstream formats (like polars or duckdb). The python package has minimal dependencies and only requires Polars. Biobear can be used to read various bioinformatic file formats, including FASTA, FASTQ, VCF, BAM, and GFF locally or from an object store like S3. It can also query some indexed file formats locally like VCF and BAM. Please see the [documentation] for information on how to get started using biobear. Quickstart To install biobear, run: Create a file with some GFF data: Then you can use biobear to read a file: This will print: Using a Session w/ Exon BioBear exposes a session object that can be used with [exon][] to work with files directly in SQL, then eventually convert them to a DataFrame if needed. See the [BioBear Docs][documentation] for more information, but in short, you can use the session like this: Ecosystem BioBear aims to make it simple to move easily to and from different prominent data tools in Python. Generally, if the tool can read Arrow or Polars, it can read BioBear's output. To see examples of how to use BioBear with other tools, see: [DuckDB][DuckDB Integration] [GenomicRanges] [DeltaLake] Performance Please see the [exon][]'s performance metrics for thorough benchmarks, but in short, biobear is generally faster than other Python libraries for reading bioinformatic file formats. For exam","default_branch":null,"files":null,"tree":[],"storefront":"/r/wheretrue","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/wheretrue/biobear/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}