Python API Reference

High-level API

Data Source interface

The following functions return a data source object to read from files that may be larger than memory.

Sequence formats

oxbow.from_fasta(source[, compression, ...])	Create a FASTA file data source.
oxbow.from_fastq(source[, compression, ...])	Create a FASTQ file data source.

Alignment formats

oxbow.from_sam(source[, compression, ...])	Create a SAM file data source.
oxbow.from_bam(source[, compression, ...])	Create a BAM file data source.
oxbow.from_cram(source, *[, fields, ...])	Create a CRAM file data source.

Variant call formats

oxbow.from_vcf(source[, compression, ...])	Create a VCF file data source.
oxbow.from_bcf(source[, compression, ...])	Create a BCF file data source.

Interval feature formats

oxbow.from_gtf(source[, compression, ...])	Create a GTF file data source.
oxbow.from_gff(source[, compression, ...])	Create a GFF3 file data source.
oxbow.from_bed(source[, bed_schema, ...])	Create a BED file data source.

UCSC BBI formats

oxbow.from_bigwig(source, *[, fields, ...])	Create a BigWig file data source.
oxbow.from_bigbed(source[, schema, fields, ...])	Create a BigBed file data source.

Arrow IPC readers

The following functions convert genomic file formats to the Arrow IPC (aka Feather) format as raw bytes. Indexed files support genomic range queries.

Arrow IPC readers

oxbow.read_fasta(src[, regions, index, gzi, ...])	Return Arrow IPC format from a FASTA file.
oxbow.read_fastq(src[, fields, compressed])	Return Arrow IPC format from a FASTQ file.
oxbow.read_sam(src[, region, index, fields, ...])	Return Arrow IPC format from a SAM file.
oxbow.read_bam(src[, region, index, fields, ...])	Return Arrow IPC format from a BAM file.
oxbow.read_cram(src[, region, index, ...])	Return Arrow IPC format from a CRAM file.
oxbow.read_vcf(src[, region, index, fields, ...])	Return Arrow IPC format from a VCF file.
oxbow.read_bcf(src[, region, index, fields, ...])	Return Arrow IPC format from a BCF file.
oxbow.read_gtf(src[, region, index, fields, ...])	Return Arrow IPC format from a GTF file.
oxbow.read_gff(src[, region, index, fields, ...])	Return Arrow IPC format from a GFF file.
oxbow.read_bed(src, bed_schema[, region, ...])	Return Arrow IPC format from a BED file.
oxbow.read_bigwig(src[, region, fields])	Return Arrow IPC format from a BigWig file.
oxbow.read_bigbed(src[, bed_schema, region, ...])	Return Arrow IPC format from a BigBed file.

Low-level API

Scanners

The following classes are wrappers of the Rust “scanner” objects that can read a genomic file format as a stream of Apache Arrow RecordBatches.

oxbow.core.PyFastaScanner(src[, compressed, ...])	A FASTA file scanner.
oxbow.core.PyFastqScanner(src[, compressed, ...])	A FASTQ file scanner.
oxbow.core.PySamScanner(src[, compressed, ...])	A SAM file scanner.
oxbow.core.PyBamScanner(src[, compressed, ...])	A BAM file scanner.
oxbow.core.PyCramScanner(src[, compressed, ...])	A CRAM file scanner.
oxbow.core.PyVcfScanner(src[, compressed, ...])	A VCF file scanner.
oxbow.core.PyBcfScanner(src[, compressed, ...])	A BCF file scanner.
oxbow.core.PyGtfScanner(src[, compressed, ...])	A GTF file scanner.
oxbow.core.PyGffScanner(src[, compressed, ...])	A GFF file scanner.
oxbow.core.PyBedScanner(src, bed_schema[, ...])	A BED file scanner.
oxbow.core.PyBigWigScanner(src[, fields, coords])	A BigWig file scanner.
oxbow.core.PyBigBedScanner(src[, schema, ...])	A BigBed file scanner.
oxbow.core.PyBBIZoomScanner(src, bbi_type, ...)	A BBI file zoom level scanner.

PyArrow adapters

The following classes provide a PyArrow Dataset interface over a stream of Arrow RecordBatches supplied by Oxbow’s low-level scanners. PyArrow Datasets allow working with large datasets that do not fit in memory.

oxbow.arrow.BatchReaderFragment(...[, ...])	A Fragment that emits RecordBatches from a reproducible source.
oxbow.arrow.BatchReaderDataset(fragments[, ...])	A PyArrow Dataset composed of one or more BatchReaderFragments.

Data source classes

oxbow.core.FastaFile(source[, compressed, ...])
oxbow.core.FastqFile(source[, compressed, ...])
oxbow.core.SamFile(source[, compressed, ...])
oxbow.core.BamFile(source[, compressed, ...])
oxbow.core.CramFile(source[, compressed, ...])
oxbow.core.VcfFile(source[, compressed, ...])
oxbow.core.BcfFile(source[, compressed, ...])
oxbow.core.GtfFile(source[, compressed, ...])
oxbow.core.GffFile(source[, compressed, ...])
oxbow.core.BedFile(source[, bed_schema, ...])
oxbow.core.BigWigFile(source, *[, fields, ...])
oxbow.core.BigBedFile(source[, schema, ...])