A tool to manage complete (bacterial) genomes from the NCBI.
Most current release is 0.1.2 (download).
- GenomeBaser:
- Encourages best practice (uses rsync -> only update what's needed),
- Despises filenames that aren't easy to understand (symlinks from RefSeq based filename to Genus_species_strain.gbk),
- Gives you what you will (probably) want in the future (provides both .gbk and .fna. Generates PROKKA databases), and
- Understands important differences (partitions complete chromosome and complete plasmid into separate directories).
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
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.