Metadata-Version: 1.1
Name: genomepy
Version: 0.2.2
Summary: Genomes in Python
Home-page: https://github.com/simonvh/genomepy
Author: Simon van Heeringen
Author-email: simon.vanheeringen@gmail.com
License: MIT
Description: genomepy
        ========
        
        |PyPI version| |Build Status| |Code Health|
        
        Easily install and use genomes in Python and elsewhere!
        
        The goal is to have a *simple* and *straightforward* way to download and
        use genomic sequences. Currently, genomepy supports UCSC, Ensembl and
        NCBI.
        
        Installation
        ------------
        
        Via pip, for now.
        
        ::
        
            $ pip install genomepy
        
        Configuration
        -------------
        
        By default genomes will be saved in ``~/.local/share/genomes``. This
        default can be changed by creating a configuration file called
        ``~/.config/genomepy/genomepy.yaml``. For instance, to set the default
        genome directory to ``/data/genomes``, edit
        ``~/.config/genomepy/genomepy.yaml`` and add the following line:
        
        ::
        
            genome_dir: /data/genomes
        
        The genome directory can also be explicitly specified in both the Python
        API as well as on the command-line.
        
        Usage
        -----
        
        From Python
        ~~~~~~~~~~~
        
        .. code:: python
        
            >>> import genomepy
            >>> for row in genomepy.search("GRCh38"):
            ...     print("\t".join(row))
            ...
            UCSC    hg38    Human Dec. 2013 (GRCh38/hg38) Genome at UCSC
            NCBI    GRCh38.p10  Homo sapiens; Genome Reference Consortium
            NCBI    GRCh38  Homo sapiens; Genome Reference Consortium
            NCBI    GRCh38.p1   Homo sapiens; Genome Reference Consortium
            NCBI    GRCh38.p2   Homo sapiens; Genome Reference Consortium
            NCBI    GRCh38.p3   Homo sapiens; Genome Reference Consortium
            NCBI    GRCh38.p4   Homo sapiens; Genome Reference Consortium
            NCBI    GRCh38.p5   Homo sapiens; Genome Reference Consortium
            NCBI    GRCh38.p6   Homo sapiens; Genome Reference Consortium
            NCBI    GRCh38.p7   Homo sapiens; Genome Reference Consortium
            NCBI    GRCh38.p8   Homo sapiens; Genome Reference Consortium
            NCBI    GRCh38.p9   Homo sapiens; Genome Reference Consortium
            Ensembl GRCh38.p10  Human
            >>> genomepy.install_genome("hg38", "UCSC", genome_dir="/data/genomes")
            downloading...
            done...
            name: hg38
            fasta: /data/genomes/hg38/hg38.fa
            >>> g = genomepy.genome("hg38", genome_dir="/data/genomes")
            >>> g["chr6"][166502000:166503000]
            tgtatggtccctagaggggccagagtcacagagatggaaagtggatggcgggtgccgggggctggggagctactgtgcagggggacagagctttagttctgcaagatgaaacagttctggagatggacggtggggatgggggcccagcaatgggaacgtgcttaatgccactgaactgggcacttaaacgtggtgaaaactgtaaaagtcatgtgtatttttctacaattaaaaaaaATCTGCCACAGAGTTAAAAAAATAACCACTATTTTCTGGAAATGGGAAGGAAAAGTTACAGCATGTAATTAAGATGACAATTTATAATGAACAAGGCAAATCTTTTCATCTTTGCCTTTTGGGCATATTCAATCTTTGCCCAGAATTAAGCACCTTTCAAGATTAATTCTCTAATAATTCTAGTTGAACAACACAACCTTTTCCTTCAAGCTTGCAATTAAATAAGGCTATTTTTAGCTGTAAGGATCACGCTGACCTTCAGGAGCAATGAGAACCGGCACTCCCGGCCTGAGTGGATGCACGGGGAGTGTGTCTAACACACAGGCGTCAACAGCCAGGGCCGCACGAGGAGGAGGAGTGGCAACGTCCACACAGACTCACAACACGGCACTCCGACTTGGAGGGTAATTAATACCAGGTTAACTTCTGGGATGACCTTGGCAACGACCCAAGGTGACAGGCCAGGCTCTGCAATCACCTCCCAATTAAGGAGAGGCGAAAGGGGACTCCCAGGGCTCAGAGCACCACGGGGTTCTAGGTCAGACCCACTTTGAAATGGAAATCTGGCCTTGTGCTGCTGCTCTTGTGGGGAGACAGCAGCTGCGGAGGCTGCTCTCTTCATGGGATTACTCTGGATAAAGTCTTTTTTGATTCTACgttgagcatcccttatctgaaatgcctgaaaccggaagtgtttaggatttggggattttgcaatatttacttatatataatgagatatcttggagatgggccacaa
        
        The ``genomepy.genome()`` method returns a ``pyfaidx.Fasta`` object, see
        the `documentation <https://github.com/mdshw5/pyfaidx>`__ for more
        examples on how to use this.
        
        Command line
        ~~~~~~~~~~~~
        
        ::
        
            $ genomepy
        
            Usage: genomepy [OPTIONS] COMMAND [ARGS]...
        
            Options:
              --help  Show this message and exit.
        
            Commands:
              genomes    list available genomes
              install    install genome
              providers  list available providers
              search     search for genomes
        
        List available genomes.
        
        ::
        
            $ genomepy genomes -p UCSC
            UCSC    hg38    Human Dec. 2013 (GRCh38/hg38) Genome at UCSC
            UCSC    hg19    Human Feb. 2009 (GRCh37/hg19) Genome at UCSC
            UCSC    hg18    Human Mar. 2006 (NCBI36/hg18) Genome at UCSC
            ...
            UCSC    danRer4 Zebrafish Mar. 2006 (Zv6/danRer4) Genome at UCSC
            UCSC    danRer3 Zebrafish May 2005 (Zv5/danRer3) Genome at UCSC
        
        Install a genome.
        
        ::
        
            $ genomepy  install hg38 UCSC -g /data/genomes
            downloading...
            done...
            name: hg38
            fasta: /data/genomes/hg38/hg38.fa
        
        Known issues
        ------------
        
        There might be issues with specific genome sequences. Sadly, not
        everything (naming, structure, filenames) is always consistent on the
        provider end. Let me know if you encounter issues with certain
        downloads.
        
        Todo
        ----
        
        -  More tests!
        -  Caching of genome listings
        -  Automatic indexing (such as bwa)
        -  Ensembl bacteria
        
        Contributing
        ------------
        
        Contributions welcome! Send me a pull request or get in
        `touch <mailto:simon.vanheeringen@gmail.com>`__.
        
        License
        -------
        
        This module is licensed under the terms of the `MIT
        license <https://opensource.org/licenses/MIT>`__.
        
        .. |PyPI version| image:: https://badge.fury.io/py/genomepy.svg
           :target: https://badge.fury.io/py/genomepy
        .. |Build Status| image:: https://travis-ci.org/simonvh/genomepy.svg?branch=master
           :target: https://travis-ci.org/simonvh/genomepy
        .. |Code Health| image:: https://landscape.io/github/simonvh/genomepy/master/landscape.svg?style=flat
           :target: https://landscape.io/github/simonvh/genomepy/master
        
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3.3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
