pybgzf
Streaming BGZF compression with on-the-fly tabix and CSI indexing.
Install with pip or uv:
pip install pybgzf
Introduction
pybgzf writes blocked gzip (BGZF) files from Python and builds their tabix (.tbi) or CSI (.csi) index while it writes, so there is no second pass with tabix.
Its core is Rust: blocks are compressed with the multithreaded, libdeflate-backed bgzf crate and indexes are written with noodles.
It needs neither pysam nor htslib.
Quick Start
Write sorted BED lines as text and the index appears next to the file on close:
>>> from pathlib import Path
>>> from tempfile import mkdtemp
>>>
>>> import pybgzf
>>> from pybgzf import Columns, IndexFormat
>>>
>>> directory = Path(mkdtemp())
>>> path = directory / "features.bed.gz"
>>>
>>> with pybgzf.writer(path, index=IndexFormat.TBI, columns=Columns.BED) as handle:
... _ = handle.write("chr1\t100\t200\tgene-a\n")
... _ = handle.write("chr1\t150\t300\tgene-b\n")
... _ = handle.write("chr2\t10\t20\tgene-c\n")
>>>
>>> sorted(file.name for file in directory.iterdir())
['features.bed.gz', 'features.bed.gz.tbi']
The output is ordinary BGZF, so gzip -d, bgzip -d, and tabix features.bed.gz chr1:120-160 all read it.
Stream bytes to a pipe or any binary file object, with columns inferred from the content:
>>> import io
>>>
>>> stream = io.BytesIO()
>>> with pybgzf.BgzfWriter(stream, threads=4, index=IndexFormat.CSI, index_path=directory / "calls.csi", columns=pybgzf.INFER) as writer:
... _ = writer.write(b"##fileformat=VCFv4.3\n")
... writer.columns == Columns.VCF
True
Read the BED file back on several threads, or query a region with 0-based, half-open coordinates:
>>> with pybgzf.reader(path, threads=4) as handle:
... handle.readline()
'chr1\t100\t200\tgene-a\n'
>>> with pybgzf.IndexedReader(path) as reader:
... list(reader.query("chr1", 180, 190))
['chr1\t100\t200\tgene-a', 'chr1\t150\t300\tgene-b']
Benchmarks
Writing 200 MB of BED lines at level 6, then reading them back, on an Apple M3 Max with benchmarks/benchmark.py:
| Command | Seconds | MB/s |
|---|---|---|
gzip (stdlib) |
4.80 | 42 |
pybgzf, 1 thread, .tbi |
1.84 | 109 |
pybgzf, 4 threads, .tbi |
0.43 | 466 |
pybgzf, 16 threads, .tbi |
0.31 | 641 |
bgzip -@1 then tabix |
3.01 | 66 |
bgzip -@4 then tabix |
1.31 | 153 |
bgzip -@16 then tabix |
0.90 | 222 |
lines from gzip.open (stdlib) |
0.66 | 303 |
lines from reader, 1 thread |
0.44 | 456 |
lines from reader, 4 threads |
0.30 | 671 |
bytes from BgzfReader, 16 threads |
0.03 | 7608 |
bgzip -d -@16 |
0.03 | 7652 |
Development and Testing
See the contributing guide for more information.
The multithreaded, position-tracking writer is adapted from fgumi, and indexing follows htslib; see NOTICE.
1 maintainer
Metadata
1 maintainer
Release files for pybgzf 0.1.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| pybgzf-0.1.0.tar.gz | 145.6 kB | Details |
Built distributions (wheels)
| File | Reset | |||
|---|---|---|---|---|
| pybgzf-0.1.0-cp311-abi3-win_amd64.whl | CPython 3.11 | abi3 | Windows x86-64 | Details |
| pybgzf-0.1.0-cp311-abi3-musllinux_1_2_x86_64.whl | CPython 3.11 | abi3 | Linux musl 1.2+ x86-64 | Details |
| pybgzf-0.1.0-cp311-abi3-musllinux_1_2_aarch64.whl | CPython 3.11 | abi3 | Linux musl 1.2+ ARM64 | Details |
| pybgzf-0.1.0-cp311-abi3-manylinux_2_28_aarch64.whl | CPython 3.11 | abi3 | Linux glibc 2.28+ ARM64 | Details |
| pybgzf-0.1.0-cp311-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl | CPython 3.11 | abi3 | Linux glibc 2.17+ x86-64 | Details |
| pybgzf-0.1.0-cp311-abi3-macosx_11_0_arm64.whl | CPython 3.11 | abi3 | macOS 11.0+ ARM64 | Details |
| pybgzf-0.1.0-cp311-abi3-macosx_10_12_x86_64.whl | CPython 3.11 | abi3 | macOS 10.12+ x86-64 | Details |
Total release size: 4.5 MB
Release files / pybgzf-0.1.0.tar.gz
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