oxbow

Read specialized bioinformatic file formats as data frames in R, Python, and more.

File formats create a lot of friction for computational biologists. Oxbow is a data unification layer that aims to improve data accessibility and ease of high-performance analytics.

Data I/O is handled in Rust with features exposed to Python and R via Apache Arrow.

Learn more in our recent blog post.

API docs

oxbow.partition_from_index_file(path, chunksize)

oxbow.read_bam(path_or_file_like, region=None, index=None)

oxbow.read_bam_vpos(path_or_file_like, pos_lo, pos_hi, index=None)

oxbow.read_bcf(path_or_file_like, region=None, index=None)

oxbow.read_bcf_vpos(path_or_file_like, pos_lo, pos_hi, index=None)

oxbow.read_bigbed(path_or_file_like, region=None, fields=None)

oxbow.read_bigwig(path_or_file_like, region=None, zoom_level=None, zoom_summary_columns=None)

oxbow.read_fasta(path, region=None)

oxbow.read_fastq(path_or_file_like)

oxbow.read_gff(path_or_file_like)

oxbow.read_gtf(path_or_file_like)

oxbow.read_vcf(path_or_file_like, region=None, index=None)

oxbow.read_vcf_vpos(path_or_file_like, pos_lo, pos_hi, index=None)