Metadata-Version: 2.1
Name: ucsc-genomes-downloader
Version: 1.1.2
Summary: Python package to quickly download genomes from the UCSC.
Home-page: https://github.com/LucaCappelletti94/ucsc_genomes_downloader
Author: Luca Cappelletti
Author-email: cappelletti.luca94@gmail.com
License: MIT
Description: ucsc_genomes_downloader
        =========================================================================================
        |travis| |sonar_quality| |sonar_maintainability| |codacy|
        |code_climate_maintainability| |pip| |downloads|
        
        Python package to quickly download and work with genomes from the UCSC.
        
        How do I install this package?
        ----------------------------------------------
        As usual, just download it using pip:
        
        .. code:: shell
        
            pip install ucsc_genomes_downloader
        
        Tests Coverage
        ----------------------------------------------
        Since some software handling coverages sometime get
        slightly different results, here's three of them:
        
        |coveralls| |sonar_coverage| |code_climate_coverage|
        
        Usage examples
        --------------
        
        Simply instanziate a new genome
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        .. code:: python
        
            from ucsc_genomes_downloader import Genome
            hg19 = Genome("hg19")
        
        Downloading selected chromosomes
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        .. code:: python
        
            from ucsc_genomes_downloader import Genome
            hg19 = Genome("hg19", chromosomes=["chr1", "chr2"])
        
        Getting gaps regions
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        .. code:: python
        
            all_gaps = hg19.gaps() # Returns gaps for all chromosomes
            # Returns gaps for chromosome chrM
            chrM_gaps = hg19.gaps(chromosomes=["chrM"])
        
        Getting filled regions
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        .. code:: python
        
            all_filled = hg19.filled() # Returns filled for all chromosomes
            # Returns filled for chromosome chrM
            chrM_filled = hg19.filled(chromosomes=["chrM"])
        
        Removing genome's cache
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        .. code:: python
        
            hg19.delete()
        
        Utilities
        -------------------------------
        
        Retrieving a list of the available genomes
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        You can get a complete list of the genomes available
        from the UCSC website with the following method:
        
        .. code:: python
        
            from ucsc_genomes_downloader import get_available_genomes
            all_genomes = get_available_genomes()
        
        .. _hg19: https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.13/
        
        .. |travis| image:: https://travis-ci.org/LucaCappelletti94/ucsc_genomes_downloader.png
           :target: https://travis-ci.org/LucaCappelletti94/ucsc_genomes_downloader
           :alt: Travis CI build
        
        .. |sonar_quality| image:: https://sonarcloud.io/api/project_badges/measure?project=LucaCappelletti94_ucsc_genomes_downloader&metric=alert_status
            :target: https://sonarcloud.io/dashboard/index/LucaCappelletti94_ucsc_genomes_downloader
            :alt: SonarCloud Quality
        
        .. |sonar_maintainability| image:: https://sonarcloud.io/api/project_badges/measure?project=LucaCappelletti94_ucsc_genomes_downloader&metric=sqale_rating
            :target: https://sonarcloud.io/dashboard/index/LucaCappelletti94_ucsc_genomes_downloader
            :alt: SonarCloud Maintainability
        
        .. |sonar_coverage| image:: https://sonarcloud.io/api/project_badges/measure?project=LucaCappelletti94_ucsc_genomes_downloader&metric=coverage
            :target: https://sonarcloud.io/dashboard/index/LucaCappelletti94_ucsc_genomes_downloader
            :alt: SonarCloud Coverage
        
        .. |coveralls| image:: https://coveralls.io/repos/github/LucaCappelletti94/ucsc_genomes_downloader/badge.svg?branch=master
            :target: https://coveralls.io/github/LucaCappelletti94/ucsc_genomes_downloader?branch=master
            :alt: Coveralls Coverage
        
        .. |pip| image:: https://badge.fury.io/py/ucsc-genomes-downloader.svg
            :target: https://badge.fury.io/py/ucsc-genomes-downloader
            :alt: Pypi project
        
        .. |downloads| image:: https://pepy.tech/badge/ucsc-genomes-downloader
            :target: https://pepy.tech/badge/ucsc-genomes-downloader
            :alt: Pypi total project downloads
        
        .. |codacy|  image:: https://api.codacy.com/project/badge/Grade/79564bf70059458b8a9ee6e775f4c7d2
            :target: https://www.codacy.com/app/LucaCappelletti94/ucsc_genomes_downloader?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=LucaCappelletti94/ucsc_genomes_downloader&amp;utm_campaign=Badge_Grade
            :alt: Codacy Maintainability
        
        .. |code_climate_maintainability| image:: https://api.codeclimate.com/v1/badges/9cd5ed4d4e41892ccc9d/maintainability
            :target: https://codeclimate.com/github/LucaCappelletti94/ucsc_genomes_downloader/maintainability
            :alt: Maintainability
        
        .. |code_climate_coverage| image:: https://api.codeclimate.com/v1/badges/9cd5ed4d4e41892ccc9d/test_coverage
            :target: https://codeclimate.com/github/LucaCappelletti94/ucsc_genomes_downloader/test_coverage
            :alt: Code Climate Coverate
        
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Provides-Extra: test
