Metadata-Version: 2.1
Name: genoml
Version: 1.0.4
Summary: Machine Learning for Genomic
Home-page: https://github.com/genoml/genoml-core
Author: Sayed Hadi Hashemi
Author-email: SayedHadiHashemi@gmail.com
Maintainer: Faraz Faghri
Maintainer-email: faraz.faghri@gmail.com
License: Apache-2.0
Description: # GenoML-core
        GenoML is an Automated Machine Learning (AutoML) for Genomic. This is the core package of GenoML. 
        this repo is under development, please report any issues (bug, performance, documentation) on the [GenoML issues page](https://github.com/GenoML/genoml/issues). 
        
        Here are some quick "get started" exmaples, please checkout the additional options and details in the [Usage][] and [CLI][].
        In general, use linux or mac with python > 3.5 for best results.
        
        ## Install 
        Run:
        ~~~~
        pip install genoml
        ~~~~
        
        ## Train the ML model 
        You can use the IPDGC (International Parkinson's Disease Genomics Consortium) test data. This data is a simulation of the genetic and clinical data used for Parkinson's diagnosis in previous publications. You can find it at [IPDGC example data][].
        
        Download and unzip data:
        ~~~
        wget https://github.com/ipdgc/GenoML-Brief-Intro/raw/master/exampleData.zip
        unzip exampleData.zip 
        ~~~
        
        To train, run:
        ~~~~
        genoml-train --geno-prefix=./exampleData/training --pheno-file=./exampleData/training.pheno --model-dir=./exampleModel
        ~~~~
        
        Final tuned model and performance metrics are stored in the ```--model-dir``` directory. 
        
        ## Using the trained ML model for inference
        ~~~~
        genoml-inference --model-dir=./exampleModel --valid-dir=./exampleData --valid-geno-prefix=./exampleData/validation --valid-pheno-file=./exampleData/validation.pheno
        ~~~~
        
        Valdiation results and model performance metrics are stored in the ```--valid-dir``` directory. 
        
        > For debugging purposes, include the ```-v``` or ```-vvv``` flags at the end of a command.
        
        [usage]: https://genoml.github.io/docs/usage
        [CLI]: https://genoml.github.io/docs/cli
        [IPDGC example data]: https://github.com/ipdgc/GenoML-Brief-Intro/raw/master/exampleData.zip
        
             
        ## Report issues 
        Please report any issue or suggestions on the [GenoML issues page](https://github.com/GenoML/genoml/issues).
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Development Status :: 4 - Beta
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: POSIX
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Description-Content-Type: text/markdown
