Metadata-Version: 1.1
Name: genomepy
Version: 0.0.1
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|
        
        Easily install and use genomes in Python and elsewhere!
        
        Installation
        ------------
        
        Via pip, for now.
        
        ::
        
            $ pip install genomepy
        
        Usage
        -----
        
        .. code:: python
        
            >>> import genomepy
            >>> for row in genomepy.search("human"):
            ...     print "\t".join(row)
            ...
            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    hg17    Human May 2004 (NCBI35/hg17) Genome at UCSC
            UCSC    hg16    Human July 2003 (NCBI34/hg16) Genome at UCSC
            Ensembl bacteria_102_collection_core_34_87_1    Brucella melitensis (GCA_000988815)
            Ensembl bacteria_94_collection_core_34_87_1 Brucella suis (GCA_000875695)
            Ensembl bacteria_131_collection_core_34_87_1    Candidatus Paraburkholderia schumannianae
            Ensembl homo_sapiens_core_86_38 Human
            Ensembl pediculus_humanus_core_34_87_2  Pediculus humanus
            >>> genomepy.install_genome("hg38", "UCSC", "/data/genomes")
            downloading...
            done...
            name: hg38
            fasta: /data/genomes/hg38/hg38.fa
            >>> g = genomepy.genome("hg38", "/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 /data/genomes/
            downloading...
            done...
            name: hg38
            fasta: /data/genomes/hg38/hg38.fa
        
        Todo
        ----
        
        -  Tests!
        -  Ensembl bacteria
        -  Automatic indexing (such as bwa)
        -  Caching of UCSC/Ensembl genome listings
        -  Configurable default genome installation directory
        
        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
        
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 :: 3.6
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
