twobitreader-rs

Fast DNA sequence extraction from 2bit files, the compact genome format used by the UCSC Genome Browser.

The motivation for this package is speed. See the underlying twobitreader Rust crate for benchmarks.

pip install twobitreader-rs

Usage

from twobitreader_rs import TwobitReader

tbr = TwobitReader.open("hg38.2bit")
tbr.get("chr1", 10000, 10005)        # 'TAACC'
tbr.seq_len("chr1")                  # 248956422
tbr.names()                          # ['chr1', 'chr2', ...]

Ranges are 0-based with an exclusive end, like a Python start:end slice. Every method also has an _inclusive counterpart taking 1-based inclusive ranges, as used by GFF/GTF and genome browsers.

Concatenation helps to assemble a spliced transcript from its exons:

from twobitreader_rs import reverse_complement

tx = tbr.concat("chr6", [(1389575, 1391118), (1394695, 1395603)])
tx = reverse_complement(tx)          # if the transcript is on the minus strand

Prefetching dramatically speeds up access to "cold" files that are not yet in the page cache:

tbr.prefetch(exons)                  # tell the OS what is coming
seqs = tbr.get_batch(exons)          # reads land as the data arrives

Documentation

The Python methods closely mirror their counterparts in the Rust crate's documentation. Every Python method carries a full docstring with arguments, return values and exceptions, visible through help(TwobitReader).

License

MIT OR Apache-2.0

Project links

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MIT OR Apache-2.0
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Python >=3.9

Provides Extra

tests

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Metadata

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  • Released:
Latest release

1 maintainer

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MIT OR Apache-2.0
View SPDX License List

Requires

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Release files for twobitreader-rs 0.2.2

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twobitreader_rs-0.2.2-cp314-cp314t-win_arm64.whl 156.1 kB CPython 3.14 CPython 3.14 free-threading Windows ARM64 Details
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twobitreader_rs-0.2.2-cp314-cp314t-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 298.6 kB CPython 3.14 CPython 3.14 free-threading Linux glibc 2.17+ x86-64 Details
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twobitreader_rs-0.2.2-cp314-cp314t-macosx_11_0_arm64.whl 262.7 kB CPython 3.14 CPython 3.14 free-threading macOS 11.0+ ARM64 Details
twobitreader_rs-0.2.2-cp314-cp314t-macosx_10_12_x86_64.whl 266.1 kB CPython 3.14 CPython 3.14 free-threading macOS 10.12+ x86-64 Details
twobitreader_rs-0.2.2-cp314-cp314-win_arm64.whl 156.4 kB CPython 3.14 CPython 3.14 Windows ARM64 Details
twobitreader_rs-0.2.2-cp314-cp314-win_amd64.whl 160.7 kB CPython 3.14 CPython 3.14 Windows x86-64 Details
twobitreader_rs-0.2.2-cp314-cp314-musllinux_1_2_x86_64.whl 503.7 kB CPython 3.14 CPython 3.14 Linux musl 1.2+ x86-64 Details
twobitreader_rs-0.2.2-cp314-cp314-musllinux_1_2_aarch64.whl 472.5 kB CPython 3.14 CPython 3.14 Linux musl 1.2+ ARM64 Details
twobitreader_rs-0.2.2-cp314-cp314-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 298.5 kB CPython 3.14 CPython 3.14 Linux glibc 2.17+ x86-64 Details
twobitreader_rs-0.2.2-cp314-cp314-manylinux_2_17_aarch64.manylinux2014_aarch64.whl 294.2 kB CPython 3.14 CPython 3.14 Linux glibc 2.17+ ARM64 Details
twobitreader_rs-0.2.2-cp314-cp314-macosx_11_0_arm64.whl 263.3 kB CPython 3.14 CPython 3.14 macOS 11.0+ ARM64 Details
twobitreader_rs-0.2.2-cp314-cp314-macosx_10_12_x86_64.whl 266.2 kB CPython 3.14 CPython 3.14 macOS 10.12+ x86-64 Details
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twobitreader_rs-0.2.2-cp313-cp313-win_amd64.whl 160.4 kB CPython 3.13 CPython 3.13 Windows x86-64 Details
twobitreader_rs-0.2.2-cp313-cp313-musllinux_1_2_x86_64.whl 502.3 kB CPython 3.13 CPython 3.13 Linux musl 1.2+ x86-64 Details
twobitreader_rs-0.2.2-cp313-cp313-musllinux_1_2_aarch64.whl 471.2 kB CPython 3.13 CPython 3.13 Linux musl 1.2+ ARM64 Details
twobitreader_rs-0.2.2-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 297.7 kB CPython 3.13 CPython 3.13 Linux glibc 2.17+ x86-64 Details
twobitreader_rs-0.2.2-cp313-cp313-manylinux_2_17_aarch64.manylinux2014_aarch64.whl 292.7 kB CPython 3.13 CPython 3.13 Linux glibc 2.17+ ARM64 Details
twobitreader_rs-0.2.2-cp313-cp313-macosx_11_0_arm64.whl 262.0 kB CPython 3.13 CPython 3.13 macOS 11.0+ ARM64 Details
twobitreader_rs-0.2.2-cp313-cp313-macosx_10_12_x86_64.whl 265.0 kB CPython 3.13 CPython 3.13 macOS 10.12+ x86-64 Details
twobitreader_rs-0.2.2-cp312-cp312-win_arm64.whl 155.7 kB CPython 3.12 CPython 3.12 Windows ARM64 Details
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twobitreader_rs-0.2.2-cp312-cp312-musllinux_1_2_x86_64.whl 502.9 kB CPython 3.12 CPython 3.12 Linux musl 1.2+ x86-64 Details
twobitreader_rs-0.2.2-cp312-cp312-musllinux_1_2_aarch64.whl 471.7 kB CPython 3.12 CPython 3.12 Linux musl 1.2+ ARM64 Details
twobitreader_rs-0.2.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 298.1 kB CPython 3.12 CPython 3.12 Linux glibc 2.17+ x86-64 Details
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twobitreader_rs-0.2.2-cp312-cp312-macosx_10_12_x86_64.whl 264.7 kB CPython 3.12 CPython 3.12 macOS 10.12+ x86-64 Details
twobitreader_rs-0.2.2-cp311-cp311-win_arm64.whl 158.8 kB CPython 3.11 CPython 3.11 Windows ARM64 Details
twobitreader_rs-0.2.2-cp311-cp311-win_amd64.whl 163.0 kB CPython 3.11 CPython 3.11 Windows x86-64 Details
twobitreader_rs-0.2.2-cp311-cp311-musllinux_1_2_x86_64.whl 507.2 kB CPython 3.11 CPython 3.11 Linux musl 1.2+ x86-64 Details
twobitreader_rs-0.2.2-cp311-cp311-musllinux_1_2_aarch64.whl 475.1 kB CPython 3.11 CPython 3.11 Linux musl 1.2+ ARM64 Details
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twobitreader_rs-0.2.2-cp311-cp311-macosx_11_0_arm64.whl 266.7 kB CPython 3.11 CPython 3.11 macOS 11.0+ ARM64 Details
twobitreader_rs-0.2.2-cp311-cp311-macosx_10_12_x86_64.whl 265.4 kB CPython 3.11 CPython 3.11 macOS 10.12+ x86-64 Details
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twobitreader_rs-0.2.2-cp310-cp310-musllinux_1_2_x86_64.whl 506.9 kB CPython 3.10 CPython 3.10 Linux musl 1.2+ x86-64 Details
twobitreader_rs-0.2.2-cp310-cp310-musllinux_1_2_aarch64.whl 475.3 kB CPython 3.10 CPython 3.10 Linux musl 1.2+ ARM64 Details
twobitreader_rs-0.2.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 301.9 kB CPython 3.10 CPython 3.10 Linux glibc 2.17+ x86-64 Details
twobitreader_rs-0.2.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl 296.7 kB CPython 3.10 CPython 3.10 Linux glibc 2.17+ ARM64 Details
twobitreader_rs-0.2.2-cp310-cp310-macosx_11_0_arm64.whl 266.5 kB CPython 3.10 CPython 3.10 macOS 11.0+ ARM64 Details
twobitreader_rs-0.2.2-cp310-cp310-macosx_10_12_x86_64.whl 265.2 kB CPython 3.10 CPython 3.10 macOS 10.12+ x86-64 Details
twobitreader_rs-0.2.2-cp39-cp39-win_amd64.whl 165.4 kB CPython 3.9 CPython 3.9 Windows x86-64 Details
twobitreader_rs-0.2.2-cp39-cp39-musllinux_1_2_x86_64.whl 509.4 kB CPython 3.9 CPython 3.9 Linux musl 1.2+ x86-64 Details
twobitreader_rs-0.2.2-cp39-cp39-musllinux_1_2_aarch64.whl 477.5 kB CPython 3.9 CPython 3.9 Linux musl 1.2+ ARM64 Details
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