Metadata-Version: 2.1
Name: peaksql
Version: 0.0.4
Summary: TODO: add peaksq description
Home-page: https://github.com/vanheeringen-lab/peaksql
Author: ['Maarten van der Sande <maartenvandersande@hotmail.com>']
License: MIT
Description: *Note: This package is in active development and functionality might change or not work correctly (yet)!*
        
        # PeakSQL
        
        [![Maintainability](https://api.codeclimate.com/v1/badges/d5f1443a164eb0d64d33/maintainability)](https://codeclimate.com/github/vanheeringen-lab/peaksql/maintainability)
        [![Test Coverage](https://api.codeclimate.com/v1/badges/d5f1443a164eb0d64d33/test_coverage)](https://codeclimate.com/github/vanheeringen-lab/peaksql/test_coverage)
        ![docs](https://github.com/vanheeringen-lab/peaksql/workflows/docs/badge.svg?branch=master)
        ![continuous-integration](https://github.com/vanheeringen-lab/peaksql/workflows/continuous-integration/badge.svg?branch=master)
        ![continuous-deployment](https://github.com/vanheeringen-lab/peaksql/workflows/continuous-deployment/badge.svg?branch=master)
        
        Dynamic machine learning database for genomics. Supports common bed-like dataformats like *.bed*, and *.narrowPeak*. *bedgraph*; and the binary *bigwig* format. 
        
        ### Installation
        PeakSQL can be installed through pip:
        ```
        pip install peaksql
        ```
        Or installed from source:
        ```
        git clone https://github.com/vanheeringen-lab/peaksql
        cd peaksql
        pip install .
        ```
        
        ### Getting started
        ```
        import peaksql
        
        # paths to our files
        db_file = 'peakSQL.sqlite'  # where to store our database
        assembly = "/path/to/hg38.fa"
        data = "binding_sites.bed"
        
        # load data into database
        db = peaksql.database.DataBase(db_file)
        db.add_assembly(assembly, assembly="hg38", species="human")
        db.add_data(data, assembly="data")
        
        # now load as dataset
        dataset = peaksql.BedRegionDataSet(db_file, seq_length=101, stride=200)
        
        # use the dataset in your application
        for seq, label in dataset:
            ...
        ```
        
Platform: UNKNOWN
Classifier: Development Status :: 1 - Planning
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: POSIX :: Linux
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >3.7
Description-Content-Type: text/markdown
