twobitreader-rs 0.2.1__tar.gz

twobitreader_rs-0.2.1/CHANGELOG.md

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+# Changelog
+
+All notable changes to this project are documented here.
+
+The format follows [Keep a Changelog](https://keepachangelog.com/en/1.1.0/), and this
+project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). The Rust
+crate `twobitreader` and the Python package `twobitreader_rs` share a version number.
+
+## [Unreleased]
+
+## [0.2.1] - 2026-10-01
+
+First release of `twobitreader_rs` on PyPI. There are no library changes; 0.2.0 reached
+crates.io before the wheel-building workflow was in place, so it was never published for
+Python.
+
+### Added
+
+- Pre-built wheels on PyPI for CPython 3.9 through 3.14, including the free-threaded
+  3.14t build, across Linux (glibc and musl), macOS and Windows, each on x86_64 and
+  aarch64. A source distribution is published alongside them for any platform or
+  interpreter not covered, PyPy included.
+- A release workflow that builds and publishes those wheels when a version tag is pushed.
+- A statement on Use of AI.
+
+## [0.2.0] - 2026-10-01
+
+`twobitreader` is now available from Python as **`twobitreader_rs`**, built with PyO3 and
+published as a wheel. The Python API mirrors the Rust one, with speed close to pure Rust.
+
+### Added
+
+- **Python bindings** (`twobitreader_rs`), exposing `TwobitReader` and `reverse_complement`.
+  Available for CPython 3.9+ on Linux, macOS and Windows.
+- **Free-threaded CPython support.** The extension is marked `gil_used = false` and the
+  reader is immutable and shareable. A thread pool over batches scales across cores on a
+  free-threaded build.
+- **Type stubs** (`py.typed` and `__init__.pyi`), so editors and type checkers see full
+  signatures for the compiled module.
+- **`prefetch_inclusive`**, the 1-based counterpart of `prefetch`, which was missing.
+
+### Changed
+
+- CI moved from CircleCI to GitHub Actions, now also building and testing the Python wheel.
+
+### Security
+
+Hardened against malformed 2bit files; the issues were unbounded allocations triggered by
+a crafted file, not memory-safety defects.
+
+### Known issues
+
+- Reading a 2bit file that another process modifies concurrently yields undefined behaviour.
+
+## [0.1.1] - 2026-09-25
+
+### Changed
+
+- Documentation fixes and updated crate keywords.
+
+## [0.1.0] - 2026-09-24
+
+Initial release of the `twobitreader` crate: sequence extraction with `get`, batched
+extraction with `get_batch`, exon concatenation with `concat`, reverse complement, and
+`prefetch` for cold files. Sequence records are parsed lazily so that opening a large file
+stays cheap. No git tag was made for this version.
+
+[Unreleased]: https://github.com/andrewdelong/twobitreader-rust/compare/v0.2.1...HEAD
+[0.2.1]: https://github.com/andrewdelong/twobitreader-rust/compare/v0.2.0...v0.2.1
+[0.2.0]: https://github.com/andrewdelong/twobitreader-rust/compare/v0.1.1...v0.2.0
+[0.1.1]: https://github.com/andrewdelong/twobitreader-rust/releases/tag/v0.1.1
+[0.1.0]: https://crates.io/crates/twobitreader/0.1.0

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twobitreader_rs-0.2.1/Cargo.toml

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+[package]
+name = "twobitreader"
+version = "0.2.1"
+edition = "2024"
+authors = ["Andrew Delong <andrew.delong@gmail.com>"]
+readme = "README.md"
+description = "Fast 2bit file reader"
+repository = "https://github.com/andrewdelong/twobitreader-rust"
+license = "MIT OR Apache-2.0"
+keywords = ["2bit", "twobit", "bioinformatics", "dna", "genome"]
+categories = ["science"]
+exclude = ["tests/", "benches/", "doc/", "*.code-workspace", ".*", "BENCH.md"]
+
+[features]
+python = ["dep:pyo3", "dep:scopeguard"]
+
+[dependencies]
+byteorder = "1"
+memmap2 = "0"
+seq-macro = "0"
+pyo3 = { version = "0", optional = true }
+scopeguard = { version = "1", optional = true}
+
+# Apple targets need fcntl(F_RDADVISE) to prefetch file ranges; madvise does not work there.
+[target.'cfg(target_vendor = "apple")'.dependencies]
+libc = "0"
+
+# Windows targets need PrefetchVirtualMemory to prefetch file ranges.
+[target.'cfg(windows)'.dependencies]
+windows-sys = { version = "0", features = ["Win32_System_Memory", "Win32_System_Threading"] }
+
+[dev-dependencies]
+flate2 = "1"
+itertools = ">=0.13, <1.0"
+rayon = "1"
+
+# Cold benchmarks use fcntl(F_NOCACHE) to write an uncached copy of the 2bit file.
+[target.'cfg(target_vendor = "apple")'.dev-dependencies]
+libc = "0"
+
+[package.metadata.docs.rs]
+rustdoc-args = ["--extend-css", "custom.css"]

twobitreader_rs-0.2.1/LICENSE-APACHE

@@ -0,0 +1,13 @@
+Copyright (c) 2023 Andrew Delong
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+	http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.

twobitreader_rs-0.2.1/LICENSE-MIT

@@ -0,0 +1,25 @@
+Copyright (c) 2023 Andrew Delong
+
+Permission is hereby granted, free of charge, to any
+person obtaining a copy of this software and associated
+documentation files (the "Software"), to deal in the
+Software without restriction, including without
+limitation the rights to use, copy, modify, merge,
+publish, distribute, sublicense, and/or sell copies of
+the Software, and to permit persons to whom the Software
+is furnished to do so, subject to the following
+conditions:
+
+The above copyright notice and this permission notice
+shall be included in all copies or substantial portions
+of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF
+ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED
+TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
+PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT
+SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
+CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR
+IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.

twobitreader_rs-0.2.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: twobitreader-rs
+Version: 0.2.1
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Operating System :: MacOS
+Classifier: Operating System :: Microsoft :: Windows
+Classifier: Development Status :: 4 - Beta
+Classifier: Programming Language :: Rust
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Programming Language :: Python :: Implementation :: CPython
+Classifier: Programming Language :: Python :: Free Threading :: 2 - Beta
+Classifier: Typing :: Typed
+Requires-Dist: pytest ; extra == 'tests'
+Provides-Extra: tests
+License-File: LICENSE-MIT
+License-File: LICENSE-APACHE
+Summary: Python bindings for the twobitreader Rust crate
+License-Expression: MIT OR Apache-2.0
+Requires-Python: >=3.9

twobitreader_rs-0.2.1/README.md

@@ -0,0 +1,132 @@
+# twobitreader
+
+
+This crate provides fast DNA sequence extraction from 2bit files, a
+[standard format](http://genome.ucsc.edu/FAQ/FAQformat.html#format7) in bioinformatics.
+
+The motivation for `twobitreader` is speed; see benchmarks below.
+It is also available as a Python package `twobitreader_rs`.
+
+The focus is raw reading from 2bit, but fast concatenation and reverse-complement methods
+are also provided to make higher-level use cases easier.
+
+[![CI](https://github.com/andrewdelong/twobitreader-rust/actions/workflows/ci.yml/badge.svg)](https://github.com/andrewdelong/twobitreader-rust/actions/workflows/ci.yml)
+ 
+![Windows](https://img.shields.io/badge/Windows-supported-blue?logo=windows)
+![macOS](https://img.shields.io/badge/macOS-supported-blue?logo=apple)
+![Linux](https://img.shields.io/badge/Linux-supported-blue?logo=linux)
+
+## Examples
+
+**Extracting sequences** is straightforward:
+```rust
+let tbr = TwobitReader::open("hg38.2bit")?; // Human genome, build 38
+let seq = tbr.get("chr1", 10000, 10005);    // -> String ("TAACC")
+```
+
+**Concatenation** works by iterating over (start, end) pairs.
+For example, assembling a spliced transcript:
+```rust
+// Exon ranges for human FKHL6 gene transcript (Gencode v43)
+let exons = [(1389575, 1391118),             // Exon 1 (start, end)
+             (1394695, 1395603)];            // Exon 2 (start, end)
+let transcript = tbr.concat("chr6", &exons); // -> String
+```
+
+**Parallelism** is easy with crates like [`rayon`](https://docs.rs/rayon/latest/rayon/).
+For example, batch extraction of sequences:
+```rust
+use rayon::prelude::*;
+let args = [("chr1", 10000, 15000),
+            ("chr1", 30000, 35000), /* ... */ ];
+let seqs = args.into_par_iter()
+    .map(|(chrom, start, end)| tbr.get(chrom, start, end))
+    .collect::<Vec<_>>(); // -> Vec<String>
+```
+Or, assembling a batch of spliced transcripts in parallel:
+```rust
+use twobitreader::reverse_complement;
+use rayon::prelude::*;
+
+fn stranded(seq: String, strand: char) -> String {
+    if strand == '+' { seq } else { reverse_complement(seq) }
+}
+
+let transcripts = [                   // (transcript_id, chromosome, exons)
+    ("ENST00000407983.7", "chr2", '+', vec![(264899, 265007),     // Exon 1
+                                            (271865, 271939),     // Exon 2
+                                            (272036, 272557)]),   // Exon 3
+    ("ENST00000319331.4", "chr3", '+', vec![(3799430, 3799919),   // Exon 1
+                                            (3844363, 3849834)]), // Exon 2
+    /* ... */
+];
+// Concatenate exons and reverse-complement if negative strand.
+// (Correct when exons are listed in genome-coordinate order.)
+let seqs = transcripts.into_par_iter()
+    .map(|(id, chrom, strand, exons)| (id, stranded(tbr.concat(chrom, exons), strand)))
+    .collect::<HashMap<_, _>>();      // HashMap<&str, String>
+let seq = &seqs["ENST00000407983.7"]; // -> &String to transcript sequence
+```
+
+**Cold files** are an order of magnitude slower to access than files already in memory ("hot").
+Use prefetching to dramatically improve single-threaded speed:
+```rust
+let exons = [("chr1", 10000, 10200),
+             ("chr1", 10500, 10700), /* ... */ ];
+tbr.prefetch(&exons);             // Ask the operating system to start paging this data from disk.
+let seqs = tbr.get_batch(&exons); // Access the memory as it arrives.
+```
+
+## Benchmarks
+
+Two tasks were benchmarked:
+- **exons**: extract 133,388 distinct human exon sequences;
+- **transcripts**: concatenate 319,468 exons into 29,211 human spliced transcript sequences.
+
+Speed depends on parallelism and page cache (hot vs cold):
+- **hot** runs represent repeated or interactive dna extraction scenarios;
+- **cold** runs represent a first run of a genomics pipeline, bound by disk speed;
+- **prefetch** runs are cold but with a `prefetch` call preceding extraction.
+
+The table below shows running times in milliseconds. Experimental details are `BENCH.md`.
+This crate provides *twobitreader* (pure rust) and *twobitreader_rs* (python wrapper).
+
+| EXONS | 1-thread / hot | 1-thread / cold | 1-thread / prefetch | 16-thread / hot | 16-thread / cold |
+|---|---:|---:|---:|---:|---:|
+| **twobitreader** (rs)        | 90    | 1,700  | 180 | 10    | 190   |
+| **twobitreader_rs** (rs, py) | 100   | 1,900  | 190 | *27   | *210  |
+| **py2bit** (c, py)           | 220   | 2,800  | n/a | n/a   | n/a   |
+| **GenomeKit** (cpp, py)      | 340   | 2,400  | n/a | n/a   | n/a   |
+| **twobit** (rs)              | 390   | 3,500  | n/a | n/a   | n/a   |
+| **twobitToFa** (c)           | 1,000 | 4,500  | n/a | 340   | 850   |
+| **twobitreader** (py)        | 7,200 | 13,000 | n/a | 1,900 | 2,300 |
+| **Biopython** (py)           | 8,100 | 11,000 | n/a | n/a   | n/a   |
+
+| TRANSCRIPTS | 1-thread / hot | 1-thread / cold | 1-thread / prefetch | 16-thread / hot | 16-thread / cold |
+|---|---:|---:|---:|---:|---:|
+| **twobitreader** (rs)        | 140    | 1,700  | 230 | 13    | 190   |
+| **twobitreader_rs** (rs, py) | 180    | 2,100  | 310 | *27   | *220  |
+| **py2bit** (c, py)           | 490    | 3,600  | n/a | n/a   | n/a   |
+| **GenomeKit** (cpp, py)      | 720    | 2,900  | n/a | n/a   | n/a   |
+| **twobit** (rs)              | 930    | 1,900  | n/a | n/a   | n/a   |
+| **twobitToFa** (c)           | 2,100  | 6,900  | n/a | 840   | 1,200 |
+| **twobitreader** (py)        | 13,000 | 21,000 | n/a | 2,800 | 3,500 |
+| **Biopython** (py)           | 19,000 | 25,000 | n/a | n/a   | n/a   |
+
+Entries marked * were run in free-threaded Python.
+
+## Dependencies
+
+* `byteorder` for handling endian-ness
+* `memmap2` for memory mapping the 2bit file
+* `seq-macro` for generating 2bit decoder lookup table
+* `libc` for prefetching file ranges on Apple targets
+* `windows-sys` for prefetching file ranges on Windows targets
+
+## Use of AI
+
+Claude Code: generated the OS-specific prefetch loops; improved handling of corrupt or malicious files;
+documented the Python bindings and mirrored their tests and benchmark; improved error checking and
+propagation to Python more broadly; and generated the CI configurations.
+
+License: MIT OR Apache-2.0

twobitreader_rs-0.2.1/custom.css

@@ -0,0 +1,28 @@
+  /*
+  Custom CSS to finesse the font sizes of inline code and block-formatted code.
+  To build docs with this CSS, first build all docs (including those of dependencies)
+  as usual, then separately build the docs for this crate with --html-in-header:
+
+    $ cargo doc
+    $ RUSTDOCFLAGS="--extend-css src/docs/custom.css" cargo doc --no-deps 
+
+  */
+
+  body {
+    font-family: sans-serif;
+  }
+
+  /* inline code (` `) */
+  code {
+    font-size: 0.9em;
+  }
+
+  /* block formatted code (``` ```)*/
+  pre {
+    padding: 6px;
+    line-height: 1.25;
+  }
+
+  pre code {
+    font-size: 0.9em;
+  }

twobitreader_rs-0.2.1/pyproject.toml

@@ -0,0 +1,40 @@
+[build-system]
+requires = ["maturin>=1.15,<2.0"]
+build-backend = "maturin"
+
+[project]
+name = "twobitreader-rs"
+description = "Python bindings for the twobitreader Rust crate"
+requires-python = ">=3.9"
+classifiers = [
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Intended Audience :: Science/Research",
+    "Operating System :: POSIX :: Linux",
+    "Operating System :: MacOS",
+    "Operating System :: Microsoft :: Windows",
+    "Development Status :: 4 - Beta",
+    "Programming Language :: Rust",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3 :: Only",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
+    "Programming Language :: Python :: Implementation :: CPython",
+    "Programming Language :: Python :: Free Threading :: 2 - Beta",
+    "Typing :: Typed",
+]
+dynamic = ["version"]
+license = "MIT OR Apache-2.0"
+license-files = ["LICENSE-MIT", "LICENSE-APACHE"]
+
+[project.optional-dependencies]
+tests = [
+    "pytest",
+]
+
+[tool.maturin]
+features = ["python"]
+module-name = "twobitreader_rs"