| Name | rustbam JSON |
| Version |
0.1.8
JSON |
| download |
| home_page | None |
| Summary | A Rust-based BAM depth calculator for Python. |
| upload_time | 2025-02-05 16:41:58 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.7 |
| license | MIT |
| keywords |
bam
bioinformatics
genomics
rust
parallel
|
| VCS |
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| bugtrack_url |
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| requirements |
No requirements were recorded.
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# 🦀 `rustbam` - Rust-powered fast BAM depth extraction with Python bindings
**rustbam** is a high-performance BAM depth calculator written in **Rust**, with **Python bindings** for fast and efficient genomic data analysis.
## 📦 Installation
### **Install from PyPI (No Conda Required)**
You can install `rustbam` directly with `pip`:
```
pip install rustbam
```
## 🛠️ Usage
### **Python API**
After installation, you can use `rustbam` in Python:
```bash
import rustbam
positions, depths = rustbam.get_depths(
bam_path, # path to bam file
chromosome, # chromosome/contig name
start, # 1-based inclusive start coordinate
end, # 1-based inclusive end coordinate
step=10, # step as in range(start, end, step) - default: 1
min_mapq=0, # minimum mapping quality - default 0
min_bq=13, # minimum base quality - default 13 (as in samtools mpileup)
max_depth=8000, # maximum depth to return per base position
num_threads=12, # number of threads for parallelization
)
print(positions[:5]) # e.g. [100000, 100010, 100020, 100030, 100040]
print(depths[:5]) # e.g. [12, 15, 10, 8, 20]
```
### **CLI (Command Line Interface)**
After installation, you can use `rustbam` in your shell (note that coordinates are 1-based and inclusive, as in `samtools mpileup`):
```bash
$ rustbam --help
usage: rustbam [-h] [-t STEP] [-Q MIN_MAPQ] [-q MIN_BQ] [-d MAX_DEPTH] [-n NUM_THREADS] [-j] bam chromosome start end
Compute sequencing depth from a BAM file.
positional arguments:
bam Path to the indexed BAM file
chromosome Chromosome name (e.g., 'chr1')
start Start position (1-based)
end End position (1-based)
options:
-h, --help show this help message and exit
-t STEP, --step STEP Step size for sampling positions (default: 1)
-Q MIN_MAPQ, --min_mapq MIN_MAPQ
Minimum mapping quality (default: 0)
-q MIN_BQ, --min_bq MIN_BQ
Minimum base quality (default: 13)
-d MAX_DEPTH, --max_depth MAX_DEPTH
Maximum depth allowed (default: 8000)
-n NUM_THREADS, --num_threads NUM_THREADS
Number of threads (default: 12)
-j, --json Output results in JSON format
```
An example usage of the CLI:
```bash
$ rustbam tests/example.bam chr1 1000000 1000005
1000000 51
1000001 52
1000002 44
1000003 52
1000004 53
1000005 47
```
You can get much faster depths result compared to samtools mpileup (as long as you use the multithreading option, `-n`):
```bash
$ time samtools mpileup /path/to/a/large/bam -r chr1:1-30000000 > /dev/null
[mpileup] 1 samples in 1 input files
real 0m52.897s
user 0m52.270s
sys 0m0.436s
$ time rustbam /path/to/a/large/bam chr1 1 30000000 -n 12 > /dev/null
real 0m18.725s
user 0m50.806s
sys 0m6.303s
```
Don't even get me started about `pysam` (about 16x faster with `-n 12`, which is the default option). 😠
---
## 🔥 Features
✅ **Fast**: Uses Rust’s efficient `rust-htslib` for BAM processing, and supports parallelism.
✅ **Python bindings**: Seamless integration with Python via `pyo3`.
✅ **Custom filtering**: Supports read quality (`-q`), base quality (`-Q`), and max depth (`-d`).
✅ **Supports large BAM files**: Uses `IndexedReader` for efficient region querying.
---
## 📜 License
`rustbam` is released under the **MIT License**. See LICENSE for details.
---
## 🤝 Contributing
1. Fork the repo on GitHub.
2. Create a new branch: `git checkout -b feature-new`
3. Commit your changes: `git commit -m "Add new feature"`
4. Push to your branch: `git push origin feature-new`
5. Open a **Pull Request** 🎉
---
## 🌍 Acknowledgments
Built using **[rust-htslib](https://github.com/rust-bio/rust-htslib)** and **[pyo3](https://github.com/PyO3/pyo3)**.
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"description": "# \ud83e\udd80 `rustbam` - Rust-powered fast BAM depth extraction with Python bindings\n\n**rustbam** is a high-performance BAM depth calculator written in **Rust**, with **Python bindings** for fast and efficient genomic data analysis.\n\n## \ud83d\udce6 Installation \n\n### **Install from PyPI (No Conda Required)** \n\nYou can install `rustbam` directly with `pip`:\n\n```\npip install rustbam\n```\n\n## \ud83d\udee0\ufe0f Usage\n\n### **Python API**\n\nAfter installation, you can use `rustbam` in Python:\n\n```bash\nimport rustbam\n\npositions, depths = rustbam.get_depths(\n bam_path, # path to bam file\n chromosome, # chromosome/contig name\n start, # 1-based inclusive start coordinate\n end, # 1-based inclusive end coordinate\n step=10, # step as in range(start, end, step) - default: 1\n min_mapq=0, # minimum mapping quality - default 0\n min_bq=13, # minimum base quality - default 13 (as in samtools mpileup)\n max_depth=8000, # maximum depth to return per base position\n num_threads=12, # number of threads for parallelization\n)\n\nprint(positions[:5]) # e.g. [100000, 100010, 100020, 100030, 100040]\nprint(depths[:5]) # e.g. [12, 15, 10, 8, 20]\n```\n\n\n### **CLI (Command Line Interface)**\n\nAfter installation, you can use `rustbam` in your shell (note that coordinates are 1-based and inclusive, as in `samtools mpileup`):\n\n```bash\n$ rustbam --help\nusage: rustbam [-h] [-t STEP] [-Q MIN_MAPQ] [-q MIN_BQ] [-d MAX_DEPTH] [-n NUM_THREADS] [-j] bam chromosome start end\n\nCompute sequencing depth from a BAM file.\n\npositional arguments:\n bam Path to the indexed BAM file\n chromosome Chromosome name (e.g., 'chr1')\n start Start position (1-based)\n end End position (1-based)\n\noptions:\n -h, --help show this help message and exit\n -t STEP, --step STEP Step size for sampling positions (default: 1)\n -Q MIN_MAPQ, --min_mapq MIN_MAPQ\n Minimum mapping quality (default: 0)\n -q MIN_BQ, --min_bq MIN_BQ\n Minimum base quality (default: 13)\n -d MAX_DEPTH, --max_depth MAX_DEPTH\n Maximum depth allowed (default: 8000)\n -n NUM_THREADS, --num_threads NUM_THREADS\n Number of threads (default: 12)\n -j, --json Output results in JSON format\n```\n\nAn example usage of the CLI:\n\n```bash\n$ rustbam tests/example.bam chr1 1000000 1000005\n1000000 51\n1000001 52\n1000002 44\n1000003 52\n1000004 53\n1000005 47\n```\n\nYou can get much faster depths result compared to samtools mpileup (as long as you use the multithreading option, `-n`):\n\n```bash\n$ time samtools mpileup /path/to/a/large/bam -r chr1:1-30000000 > /dev/null\n[mpileup] 1 samples in 1 input files\n\nreal 0m52.897s\nuser 0m52.270s\nsys 0m0.436s\n\n$ time rustbam /path/to/a/large/bam chr1 1 30000000 -n 12 > /dev/null\n\nreal 0m18.725s\nuser 0m50.806s\nsys 0m6.303s\n```\n\nDon't even get me started about `pysam` (about 16x faster with `-n 12`, which is the default option). \ud83d\ude20\n\n---\n\n## \ud83d\udd25 Features\n\n\u2705 **Fast**: Uses Rust\u2019s efficient `rust-htslib` for BAM processing, and supports parallelism. \n\u2705 **Python bindings**: Seamless integration with Python via `pyo3`. \n\u2705 **Custom filtering**: Supports read quality (`-q`), base quality (`-Q`), and max depth (`-d`). \n\u2705 **Supports large BAM files**: Uses `IndexedReader` for efficient region querying.\n\n---\n\n## \ud83d\udcdc License\n\n`rustbam` is released under the **MIT License**. See LICENSE for details.\n\n---\n\n## \ud83e\udd1d Contributing\n\n1. Fork the repo on GitHub.\n2. Create a new branch: `git checkout -b feature-new`\n3. Commit your changes: `git commit -m \"Add new feature\"`\n4. Push to your branch: `git push origin feature-new`\n5. Open a **Pull Request** \ud83c\udf89\n\n---\n\n## \ud83c\udf0d Acknowledgments\n\nBuilt using **[rust-htslib](https://github.com/rust-bio/rust-htslib)** and **[pyo3](https://github.com/PyO3/pyo3)**.\n\n\n",
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