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GenomeBaser manages complete (bacterial) genomes from NCBI

Project description

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

Most current release is 0.1.1.

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/v0.1.1.tar.gz
$ tar -zxvf v0.1.1.tar.gz
$ cd v0.1.1
$ # May need sudo/root, BUT...
$ python setup.py install

Usage

Something like:

python genomebaser.py 'Pseudomonas aeruginosa' ~/dbs

Project details


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