Metadata-Version: 2.1
Name: MiScan
Version: 0.1a1
Summary: Maxout-inferred SNV-based cancer prediction model
Home-page: UNKNOWN
Author: Qulab USTC
Author-email: jeffery_cpu@163.com
License: UNKNOWN
Project-URL: MiScan website, http://galaxy.ustc.edu.cn
Keywords: deep learning SNV breast cancer prediction
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Education
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Healthcare Industry
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: POSIX :: Linux
Classifier: Natural Language :: English
Requires-Python: >=3.4
Description-Content-Type: text/markdown
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Requires-Dist: Werkzeug (==0.15.5)
Requires-Dist: wrapt (==1.11.2)

# MiScan_core

Maxout-inferred SNV-based cancer prediction model | Apache Software License

# Tutorial

### installation

- install through `pip`

```bash
pip install MiScan -i https://pypi.python.org/pypi
```

- install through docker

```bash
docker pull jefferyustc/miscan_command_line:v0.2.1
```



### usage-commandline



```bash
miscan --vcf /Users/jeffery/Downloads/SRR5447191.combined.filtered.vcf -o outputs --weight /Users/jeffery/workspace/projects/outputs/_MiScan_weights.hdf5
```

or with below command:

```bash
python -m MiScan --vcf /Users/jeffery/Downloads/SRR5447191.combined.filtered.vcf -o outputs --weight /Users/jeffery/workspace/projects/outputs/_MiScan_weights.hdf5
```

if with docker:

```bash
docker run --name miscan_cli_test -it -v /path/to/data:/path/in/docker 9fd
MiScan -o test_outputs --vcf ../model/SRR5447191.combined.filtered.vcf --weight ../model/_MiScan_weights.hdf5
```



### usage-script



```python
from MiScan import miscan_main

miscan_main(
    outDir='./outputs',
    inVcf='/Users/jeffery/Downloads/SRR5447191.combined.filtered.vcf',
    model_weight='/Users/jeffery/workspace/projects/outputs/_MiScan_weights.hdf5'
)
```



