Metadata-Version: 2.4
Name: merge-cli
Version: 3.7
Summary: MERGE variant pathogenicity prediction CLI with precomputed VCF cache and local/remote model integrations
Author: MERGE Team
License-Expression: LicenseRef-Proprietary
Project-URL: Homepage, https://merge.fanglab.cn
Keywords: bioinformatics,variant,pathogenicity,genomics,cli
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Environment :: Console
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.11
Description-Content-Type: text/markdown
Requires-Dist: click>=8.1
Requires-Dist: rich>=13.0
Requires-Dist: requests>=2.31
Requires-Dist: pysam>=0.22
Requires-Dist: numpy>=1.26
Requires-Dist: pandas>=2.1
Requires-Dist: scikit-learn>=1.4
Requires-Dist: joblib>=1.3
Requires-Dist: matplotlib>=3.8
Requires-Dist: shap>=0.44

# merge-cli 3.7

MERGE variant pathogenicity prediction CLI.

## Highlights

- Remote and local prediction modes.
- Local precomputed VCF cache lookup for hg38/hg19 coding and splicing variants.
- Local/remote model switches for AlphaGenome, HyenaDNA, NT, Evo2, Enformer, GENERATOR, GENERATOR-v2, and NT-v2.
- Bundled MERGE ensemble model files.

## Quick Start

```bash
pip install merge-cli
merge --help
merge predict --chrom chr1 --pos 69428 --ref T --alt G --genome hg38
```

## Precomputed VCF Cache

```bash
merge precomputed configure --data-dir /path/to/precomputed
merge precomputed status
merge precomputed download --genome all --variant-type all
```

Expected files include `coding_merged.vcf.gz`, `splicing_merged.vcf.gz`, their hg19 counterparts, and `.tbi` indices.

## GENERATOR / GENERATOR-v2 / NT-v2

These models use one external service by default at `http://127.0.0.1:18004`.

```bash
merge generator-ntv2 configure --url http://127.0.0.1:18004
merge generator-ntv2 status
merge predict --chrom chr1 --pos 69428 --ref T --alt G --generator --generator-v2 --nt-v2
```

Local mode uses the same service URL:

```bash
merge predict --local --chrom chr1 --pos 69428 --ref T --alt G --ensemble-type coding --generator --generator-v2 --nt-v2
```

Service contract:

- `GET /health`
- `POST /predict` with `chrom`, `pos`, `ref`, `alt`, `genome_version`, `models`
- `POST /batch_predict` with `variants`, `models`

Model keys: `generator`, `generator_v2`, `nt_v2`.

## Enformer

```bash
merge enformer configure --url http://localhost:5004
merge enformer status
```

If local services are unavailable, errors are reported under `prediction.errors` and the CLI continues returning available results.
