Metadata-Version: 2.0
Name: GenomeBaser
Version: 0.1.2
Summary: GenomeBaser manages complete (bacterial) genomes from NCBI
Home-page: http://github.com/mscook/GenomeBaser
Author: Mitchell Stanton-Cook
Author-email: m.stantoncook@gmail.com
License: ECL 2.0
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved
Classifier: Natural Language :: English
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 2 :: Only
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Dist: biopython
Requires-Dist: click

GenomeBaser
===========

A tool to manage complete (bacterial) genomes from the NCBI.

Most current release is 0.1.2_.


Why?
----

GenomeBaser:
    1) Encourages best practice (uses rsync -> only update what's needed)
    2) Despises filenames that aren't easily understandable (symlinks to 
       RefSeq based filename to  Genus_species_strain.gbk)
    3) Give you what you will probably wan't in the future (provides both .gbk 
       and .fna. Generate PROKKA databases)
    4) Understands important differences (partitions complete chomosome and 
       complete plasmind into separate buckets)


Installation
------------

Something like::

    $ pip install GenomeBaser

Alternatively::

    $ wget https://github.com/mscook/GenomeBaser/archive/v0.1.2.tar.gz
    $ tar -zxvf v0.1.2.tar.gz
    $ cd v0.1.2
    $ # May need sudo/root, BUT...
    $ python setup.py install


Usage
-----

Something like::

    $ GenomeBaser --help
        Usage: GenomeBaser [OPTIONS] GENUS SPECIES OUT_DATABASE_LOCATION

        GenomeBaser is tool to manage complete (bacterial) genomes from the NCBI.

        Example usage:

              $ GenomeBaser.py Klebsiella pneumoniae ~/dbs

              $ # (wait a few months)...

              $ GenomeBaser Klebsiella pneumoniae ~/dbs

        By Mitchell Stanton-Cook (m.stantoncook@gmail.com)

        **More info at:** https://github.com/mscook/GenomeBaser

        Options:
          --check_deps / --no-check_deps  Check that non-python dependencies exist
          --help                          Show this message and exit.



.. _0.1.2: https://github.com/mscook/GenomeBaser/archive/v0.1.2.tar.gz


