OctopuSV 0.2.0__tar.gz

octopusv-0.2.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2023 Yangyang Li and Qingxiang Guo
+
+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.

octopusv-0.2.0/PKG-INFO

@@ -0,0 +1,214 @@
+Metadata-Version: 2.1
+Name: OctopuSV
+Version: 0.2.0
+Summary: OctopuSV: Advanced Structural Variant Analysis Toolkit
+License: MIT
+Author: Qingxiang Guo
+Author-email: qingxiang.guo@northwestern.edu
+Requires-Python: >=3.10,<4.0
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Requires-Dist: jinja2 (>=3.1.5,<4.0.0)
+Requires-Dist: loguru (>=0.7.2,<0.8.0)
+Requires-Dist: matplotlib (>=3.9.2,<4.0.0)
+Requires-Dist: natsort (>=8.4.0,<9.0.0)
+Requires-Dist: pytest-cov (>=4.1.0,<5.0.0)
+Requires-Dist: rich (>=13.7.1,<14.0.0)
+Requires-Dist: seaborn (>=0.13.2,<0.14.0)
+Requires-Dist: typer (>=0.12.3,<0.13.0)
+Description-Content-Type: text/markdown
+
+# OctopuSV: Advanced structural variant analysis toolkit 🐙
+
+<p align="center">
+  <img src="https://github.com/ylab-hi/octopusV/blob/main/imgs/logo.png" width="40%" height="40%">
+</p>
+
+[![PyPI version](https://badge.fury.io/py/octopusv.svg)](https://badge.fury.io/py/octopusv)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+
+**OctopuSV** is a high-performance structural variant (SV) analysis toolkit designed to standardize ambiguous SV annotations (e.g., BNDs), flexibly integrate multiple callers across samples or platforms, and benchmark results against trusted truth sets. With support for both **single-sample** and **multi-sample** workflows, OctopuSV enables robust and scalable SV comparison, correction, and visualization in real or simulated genomic datasets.
+
+## Key Features
+
+* **BND Correction**: Converts ambiguous breakend (BND) records into canonical SV types (DEL, INV, DUP, TRA), with translocation subtype classification
+* **Flexible Multi-sample Merging**: Boolean logic-based merge of SVs across multiple samples or callers
+* **Multi-caller & Multi-platform Integration**: Works seamlessly across Illumina, PacBio, ONT callers like Manta, LUMPY, SvABA, DELLY, PBSV, Sniffles, etc.
+* **Benchmarking**: Compare SVs to truth sets with precision/recall/F1 metrics using GIAB-style evaluation
+* **Statistical Summaries**: Profile SV distribution, quality, and size
+* **Publication-ready Visualizations**: Output interactive HTML reports and static plots
+
+## Installation
+
+```bash
+pip install octopusv
+```
+
+---
+
+## Quick Start
+
+### 1. Correct Ambiguous BND Annotations
+
+```bash
+# Basic correction
+octopusv correct input.vcf output.vcf
+
+# With position tolerance control
+octopusv correct -i input.vcf -o output.vcf --pos-tolerance 5
+
+# Apply quality filters
+octopusv correct -i input.vcf -o output.vcf --min-svlen 50 --max-svlen 100000 --filter-pass
+```
+
+### 2. Merge SV Calls (Multi-caller or Multi-sample)
+
+```bash
+# Merge across callers from same sample
+octopusv merge -i manta.svcf lumpy.svcf -o merged.svcf --mode caller --caller-names Manta,LUMPY --intersect
+
+# Merge across samples
+octopusv merge -i sample1.svcf sample2.svcf sample3.svcf \
+  --mode sample --sample-names HG001,HG002,HG003 \
+  --min-support 2 -o shared.svcf
+
+# Complex logic: A AND B but not C
+octopusv merge -i A.svcf B.svcf C.svcf \
+  --expression "(A AND B) AND NOT C" -o result.svcf
+
+# Generate UpSet plot
+octopusv merge -i a.svcf b.svcf c.svcf -o merged.svcf --intersect --upsetr --upsetr-output intersection.png
+```
+
+<p align="center">
+  <img src="https://github.com/ylab-hi/octopusV/blob/main/imgs/up_upset.png" width="70%" height="70%">
+</p>
+
+### 3. Benchmark Against Truth Sets
+
+```bash
+octopusv benchmark truth.vcf calls.svcf \
+  -o benchmark_results \
+  --reference-distance 500 \
+  --size-similarity 0.7 \
+  --reciprocal-overlap 0.0 \
+  --size-min 50 --size-max 50000
+```
+
+### 4. Generate Statistics and Visualizations
+
+```bash
+# Basic stat collection
+octopusv stat -i input.svcf -o stats.txt
+
+# Add HTML report
+octopusv stat -i input.svcf -o stats.txt --report
+
+# Plot figures from stats
+octopusv plot stats.txt -o figure_prefix
+```
+
+The `--report` flag outputs an interactive HTML report:
+
+* SV type and size distributions
+* Chromosome breakdowns
+* Quality score summaries
+* Genotype and depth features
+
+<p align="center">
+  <img src="https://github.com/ylab-hi/octopusV/blob/main/imgs/html_example.png" width="70%" height="70%">
+</p>
+
+### 5. Format Conversion
+
+```bash
+# To BED
+octopusv svcf2bed -i input.svcf -o output.bed
+
+# To BEDPE
+octopusv svcf2bedpe -i input.svcf -o output.bedpe
+
+# To standard VCF
+octopusv svcf2vcf -i input.svcf -o output.vcf
+```
+
+---
+
+## Example Visualizations
+
+OctopusV generates publication-ready visualizations:
+
+### Chromosome Distribution
+
+<p align="center">
+  <img src="https://github.com/ylab-hi/octopusV/blob/main/imgs/chromosome_distribution.png" width="50%" height="50%">
+</p>
+
+### SV Type Distribution
+
+<p align="center">
+  <img src="https://github.com/ylab-hi/octopusV/blob/main/imgs/sv_types.png" width="50%" height="50%">
+</p>
+
+### SV Size Distribution
+
+<p align="center">
+  <img src="https://github.com/ylab-hi/octopusV/blob/main/imgs/sv_sizes.png" width="50%" height="50%">
+</p>
+
+---
+
+## Application Scenarios
+
+OctopuSV was developed to address several practical needs in SV research:
+
+* Standardizing SVs with ambiguous BND notations
+* Enabling precise cohort-level comparisons (multi-sample mode)
+* Supporting accurate benchmarking with real/simulated truth sets
+* Integrating and comparing SVs across platforms (e.g., Illumina + ONT)
+* Automating large-scale SV analysis workflows (via TentacleSV)
+
+See the companion pipeline: [TentacleSV](https://github.com/ylab-hi/TentacleSV)
+
+---
+
+## 🧪 Citation
+
+If you use **OctopuSV**, please cite:
+
+> Guo Q, Li Y, Wang T, Ramakrishnan A, Yang R. *OctopuSV and TentacleSV: a one-stop toolkit for multi-sample, cross-platform structural variant comparison and analysis*. bioRxiv. 2025. doi: [10.1101/2025.03.24.645012](https://doi.org/10.1101/2025.03.24.645012)
+
+```bibtex
+@article{guo2025octopusv,
+  title={OctopuSV and TentacleSV: a one-stop toolkit for multi-sample, cross-platform structural variant comparison and analysis},
+  author={Guo, Qingxiang and Li, Yangyang and Wang, Tingyou and Ramakrishnan, Abhi and Yang, Rendong},
+  journal={bioRxiv},
+  year={2025},
+  publisher={Cold Spring Harbor Laboratory},
+  doi={10.1101/2025.03.24.645012},
+  url={https://www.biorxiv.org/content/10.1101/2025.03.24.645012v1}
+}
+```
+
+---
+
+## Contributing
+
+We welcome issues, suggestions, and pull requests!
+
+```bash
+git clone https://github.com/ylab-hi/OctopuSV.git
+cd OctopuSV
+poetry install
+pre-commit run -a
+```
+
+## Contact
+
+* GitHub Issues: [https://github.com/ylab-hi/octopusV/issues](https://github.com/ylab-hi/octopusV/issues)
+* Email: [qingxiang.guo@northwestern.edu](mailto:qingxiang.guo@northwestern.edu)
+* Email: [yangyang.li@northwestern.edu](mailto:yangyang.li@northwestern.edu)
+

octopusv-0.2.0/README.md

@@ -0,0 +1,190 @@
+# OctopuSV: Advanced structural variant analysis toolkit 🐙
+
+<p align="center">
+  <img src="https://github.com/ylab-hi/octopusV/blob/main/imgs/logo.png" width="40%" height="40%">
+</p>
+
+[![PyPI version](https://badge.fury.io/py/octopusv.svg)](https://badge.fury.io/py/octopusv)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+
+**OctopuSV** is a high-performance structural variant (SV) analysis toolkit designed to standardize ambiguous SV annotations (e.g., BNDs), flexibly integrate multiple callers across samples or platforms, and benchmark results against trusted truth sets. With support for both **single-sample** and **multi-sample** workflows, OctopuSV enables robust and scalable SV comparison, correction, and visualization in real or simulated genomic datasets.
+
+## Key Features
+
+* **BND Correction**: Converts ambiguous breakend (BND) records into canonical SV types (DEL, INV, DUP, TRA), with translocation subtype classification
+* **Flexible Multi-sample Merging**: Boolean logic-based merge of SVs across multiple samples or callers
+* **Multi-caller & Multi-platform Integration**: Works seamlessly across Illumina, PacBio, ONT callers like Manta, LUMPY, SvABA, DELLY, PBSV, Sniffles, etc.
+* **Benchmarking**: Compare SVs to truth sets with precision/recall/F1 metrics using GIAB-style evaluation
+* **Statistical Summaries**: Profile SV distribution, quality, and size
+* **Publication-ready Visualizations**: Output interactive HTML reports and static plots
+
+## Installation
+
+```bash
+pip install octopusv
+```
+
+---
+
+## Quick Start
+
+### 1. Correct Ambiguous BND Annotations
+
+```bash
+# Basic correction
+octopusv correct input.vcf output.vcf
+
+# With position tolerance control
+octopusv correct -i input.vcf -o output.vcf --pos-tolerance 5
+
+# Apply quality filters
+octopusv correct -i input.vcf -o output.vcf --min-svlen 50 --max-svlen 100000 --filter-pass
+```
+
+### 2. Merge SV Calls (Multi-caller or Multi-sample)
+
+```bash
+# Merge across callers from same sample
+octopusv merge -i manta.svcf lumpy.svcf -o merged.svcf --mode caller --caller-names Manta,LUMPY --intersect
+
+# Merge across samples
+octopusv merge -i sample1.svcf sample2.svcf sample3.svcf \
+  --mode sample --sample-names HG001,HG002,HG003 \
+  --min-support 2 -o shared.svcf
+
+# Complex logic: A AND B but not C
+octopusv merge -i A.svcf B.svcf C.svcf \
+  --expression "(A AND B) AND NOT C" -o result.svcf
+
+# Generate UpSet plot
+octopusv merge -i a.svcf b.svcf c.svcf -o merged.svcf --intersect --upsetr --upsetr-output intersection.png
+```
+
+<p align="center">
+  <img src="https://github.com/ylab-hi/octopusV/blob/main/imgs/up_upset.png" width="70%" height="70%">
+</p>
+
+### 3. Benchmark Against Truth Sets
+
+```bash
+octopusv benchmark truth.vcf calls.svcf \
+  -o benchmark_results \
+  --reference-distance 500 \
+  --size-similarity 0.7 \
+  --reciprocal-overlap 0.0 \
+  --size-min 50 --size-max 50000
+```
+
+### 4. Generate Statistics and Visualizations
+
+```bash
+# Basic stat collection
+octopusv stat -i input.svcf -o stats.txt
+
+# Add HTML report
+octopusv stat -i input.svcf -o stats.txt --report
+
+# Plot figures from stats
+octopusv plot stats.txt -o figure_prefix
+```
+
+The `--report` flag outputs an interactive HTML report:
+
+* SV type and size distributions
+* Chromosome breakdowns
+* Quality score summaries
+* Genotype and depth features
+
+<p align="center">
+  <img src="https://github.com/ylab-hi/octopusV/blob/main/imgs/html_example.png" width="70%" height="70%">
+</p>
+
+### 5. Format Conversion
+
+```bash
+# To BED
+octopusv svcf2bed -i input.svcf -o output.bed
+
+# To BEDPE
+octopusv svcf2bedpe -i input.svcf -o output.bedpe
+
+# To standard VCF
+octopusv svcf2vcf -i input.svcf -o output.vcf
+```
+
+---
+
+## Example Visualizations
+
+OctopusV generates publication-ready visualizations:
+
+### Chromosome Distribution
+
+<p align="center">
+  <img src="https://github.com/ylab-hi/octopusV/blob/main/imgs/chromosome_distribution.png" width="50%" height="50%">
+</p>
+
+### SV Type Distribution
+
+<p align="center">
+  <img src="https://github.com/ylab-hi/octopusV/blob/main/imgs/sv_types.png" width="50%" height="50%">
+</p>
+
+### SV Size Distribution
+
+<p align="center">
+  <img src="https://github.com/ylab-hi/octopusV/blob/main/imgs/sv_sizes.png" width="50%" height="50%">
+</p>
+
+---
+
+## Application Scenarios
+
+OctopuSV was developed to address several practical needs in SV research:
+
+* Standardizing SVs with ambiguous BND notations
+* Enabling precise cohort-level comparisons (multi-sample mode)
+* Supporting accurate benchmarking with real/simulated truth sets
+* Integrating and comparing SVs across platforms (e.g., Illumina + ONT)
+* Automating large-scale SV analysis workflows (via TentacleSV)
+
+See the companion pipeline: [TentacleSV](https://github.com/ylab-hi/TentacleSV)
+
+---
+
+## 🧪 Citation
+
+If you use **OctopuSV**, please cite:
+
+> Guo Q, Li Y, Wang T, Ramakrishnan A, Yang R. *OctopuSV and TentacleSV: a one-stop toolkit for multi-sample, cross-platform structural variant comparison and analysis*. bioRxiv. 2025. doi: [10.1101/2025.03.24.645012](https://doi.org/10.1101/2025.03.24.645012)
+
+```bibtex
+@article{guo2025octopusv,
+  title={OctopuSV and TentacleSV: a one-stop toolkit for multi-sample, cross-platform structural variant comparison and analysis},
+  author={Guo, Qingxiang and Li, Yangyang and Wang, Tingyou and Ramakrishnan, Abhi and Yang, Rendong},
+  journal={bioRxiv},
+  year={2025},
+  publisher={Cold Spring Harbor Laboratory},
+  doi={10.1101/2025.03.24.645012},
+  url={https://www.biorxiv.org/content/10.1101/2025.03.24.645012v1}
+}
+```
+
+---
+
+## Contributing
+
+We welcome issues, suggestions, and pull requests!
+
+```bash
+git clone https://github.com/ylab-hi/OctopuSV.git
+cd OctopuSV
+poetry install
+pre-commit run -a
+```
+
+## Contact
+
+* GitHub Issues: [https://github.com/ylab-hi/octopusV/issues](https://github.com/ylab-hi/octopusV/issues)
+* Email: [qingxiang.guo@northwestern.edu](mailto:qingxiang.guo@northwestern.edu)
+* Email: [yangyang.li@northwestern.edu](mailto:yangyang.li@northwestern.edu)

octopusv-0.2.0/pyproject.toml

@@ -0,0 +1,185 @@
+[tool.poetry]
+name = "OctopuSV"
+version = "0.2.0"
+description = "OctopuSV: Advanced Structural Variant Analysis Toolkit"
+authors = [
+    "Qingxiang Guo <qingxiang.guo@northwestern.edu>",
+    "Yangyang Li <yangyang.li@northwestern.edu>",
+]
+license = "MIT"
+readme = "README.md"
+
+[tool.poetry.dependencies]
+python = "^3.10"
+typer = "^0.12.3"
+loguru = "^0.7.2"
+rich = "^13.7.1"
+natsort = "^8.4.0"
+pytest-cov = "^4.1.0"
+matplotlib = "^3.9.2"
+seaborn = "^0.13.2"
+jinja2 = "^3.1.5"
+
+
+[tool.poetry.scripts]
+octopusv = "octopusv.cli.cli:app"
+
+[tool.poetry.group.dev.dependencies]
+pytest-sugar = "^1.0.0"
+pytest = "^8.0.2"
+ruff = "^0.7.0"
+ipdb = "^0.13.13"
+mypy = "^1.10.0"
+
+
+[tool.ruff]
+target-version = "py310"
+line-length = 120
+fix = true
+exclude = [
+    "tasks.py",
+    "tests/*",
+    "build.py",
+    "scripts/*",
+    "noxfile.py",
+    "docs/conf.py",
+
+
+    ".bzr",
+    ".direnv",
+    ".eggs",
+    ".git",
+    ".git-rewrite",
+    ".hg",
+    ".mypy_cache",
+    ".nox",
+    ".pants.d",
+    ".pytype",
+    ".ruff_cache",
+    ".svn",
+    ".tox",
+    ".venv",
+    "__pypackages__",
+    "_build",
+    "buck-out",
+    "build",
+    "dist",
+    "node_modules",
+    "venv",
+]
+
+[tool.ruff.lint]
+select = [
+    "ANN",
+    "D",
+    "A",
+    "F",
+    "E",
+    "W",
+    "C90",
+    "I",
+    "UP",
+    "N",
+    "YTT",
+    "TID",
+    "S",
+    "BLE",
+    "FBT",
+    "PLR",
+    "B",
+    "B9",
+    "A",
+    "C4",
+    "T10",
+    "EM",
+    "ICN",
+    "T20",
+    "Q",
+    "RET",
+    "SIM",
+    "ARG",
+    "DTZ",
+    "ERA",
+    "PD",
+    "PGH",
+    "PLC",
+    "PLE",
+    "PLW",
+    "RUF",
+    "PL",
+    "TD",
+    "FIX",
+    "PTH",
+    "TCH",
+    "SLOT",
+    "PT",
+    "PYI",
+    "PIE",
+    "ISC",
+    "FA",
+    "EXE",
+    # "CPY",
+    "COM",
+    "SIM",
+]
+ignore = [
+    "E501",
+    "D203",
+    "D100",
+    "D401",
+    "ANN101",
+    "ANN102",
+    "ANN001",
+    "ANN002",
+    "ANN003",
+    "ANN201",
+    "ANN202",
+    "ANN204",
+    "ANN205",
+    "ANN206",
+    "PGH003",
+    "N802",
+    "N803",
+    "N806",
+    "N815",
+    "EM101",
+    # formater conflict
+    'COM812',
+    'COM819',
+    'D206',
+    'ISC001',
+    'Q000',
+    'Q001',
+    'Q002',
+    'Q003',
+    'W191',
+]
+
+[tool.ruff.format]
+# Like Black, use double quotes for strings.
+quote-style = "double"
+
+# Like Black, indent with spaces, rather than tabs.
+indent-style = "space"
+
+# Like Black, respect magic trailing commas.
+# magic-trailing-comma = "respect"
+
+# Like Black, automatically detect the appropriate line ending.
+line-ending = "auto"
+
+[tool.ruff.lint.flake8-bugbear]
+extend-immutable-calls = ["chr", "typer.Argument", "typer.Option"]
+
+[tool.ruff.lint.flake8-annotations]
+allow-star-arg-any = true
+
+[tool.ruff.lint.per-file-ignores]
+
+[tool.ruff.lint.pydocstyle]
+convention = 'google'
+
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"

octopusv-0.2.0/src/octopusv/__init__.py

@@ -0,0 +1,4 @@
+"""Top-level package for OctopusV."""
+
+__version__ = "0.1.0"
+__PACKAGE_NAME__ = "octopusv"

octopusv-0.2.0/src/octopusv/__main__.py

@@ -0,0 +1,3 @@
+from .cli.cli import app
+
+app()

octopusv-0.2.0/src/octopusv/bencher/bench_utils.py

@@ -0,0 +1,39 @@
+import json
+from pathlib import Path
+
+
+def calculate_metrics(results: dict[str, list]):
+    """Calculate benchmark metrics including precision, recall, and F1 score."""
+    tp = len(results["tp_call"])
+    fp = len(results["fp"])
+    fn = len(results["fn"])
+
+    precision = tp / (tp + fp) if tp + fp > 0 else 0
+    recall = tp / (tp + fn) if tp + fn > 0 else 0
+    f1 = 2 * (precision * recall) / (precision + recall) if precision + recall > 0 else 0
+
+    return {"TP": tp, "FP": fp, "FN": fn, "Precision": precision, "Recall": recall, "F1": f1}
+
+
+def write_vcf(file_path: Path, events: list[tuple | object]):
+    """Write events to VCF format file."""
+    with file_path.open("w") as f:
+        f.write("#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n")
+        for event in events:
+            if isinstance(event, tuple):  # TRA event
+                chrom, start_chrom, end_chrom, start_pos, end_pos, source_file, bnd_pattern = event
+                f.write(
+                    f"{start_chrom}\t{start_pos}\t.\tN\t{bnd_pattern}\t.\tPASS\t"
+                    f"SVTYPE=TRA;END={end_pos};CHR2={end_chrom};SOURCES={source_file}\n"
+                )
+            else:  # Other SV events
+                f.write(
+                    f"{event.chrom}\t{event.pos}\t{event.sv_id}\t{event.ref}\t{event.alt}\t"
+                    f"{event.quality}\t{event.filter}\t{';'.join(f'{k}={v}' for k, v in event.info.items())}\n"
+                )
+
+
+def write_summary(file_path: Path, metrics: dict):
+    """Write benchmark summary metrics to JSON file."""
+    with file_path.open("w") as f:
+        json.dump(metrics, f, indent=2)