GenomeBaser

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

Most current release is 0.1.2 (download).

Why?

GenomeBaser:

1. Encourages best practice (uses rsync -> only update what's needed),
2. Despises filenames that aren't easy to understand (symlinks from RefSeq based filename to Genus_species_strain.gbk),
3. Gives you what you will (probably) want in the future (provides both .gbk and .fna. Generates PROKKA databases), and
4. Understands important differences (partitions complete chromosome and complete plasmid into separate directories).

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 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.