{ "info": { "author": "Mitchell Stanton-Cook", "author_email": "m.stantoncook@gmail.com", "bugtrack_url": null, "classifiers": [ "Development Status :: 3 - Alpha", "Environment :: Console", "Intended Audience :: Science/Research", "License :: OSI Approved", "Natural Language :: English", "Operating System :: POSIX :: Linux", "Programming Language :: Python", "Programming Language :: Python :: 2.7", "Programming Language :: Python :: 2 :: Only", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "GenomeBaser\n===========\n\nA tool to manage complete (bacterial) genomes from the NCBI.\n\nMost current release is 0.1.2_.\n\n\nWhy?\n----\n\nGenomeBaser:\n 1) Encourages best practice (uses rsync -> only update what's needed)\n 2) Despises filenames that aren't easily understandable (symlinks to \n RefSeq based filename to Genus_species_strain.gbk)\n 3) Give you what you will probably wan't in the future (provides both .gbk \n and .fna. Generate PROKKA databases)\n 4) Understands important differences (partitions complete chomosome and \n complete plasmind into separate buckets)\n\n\nInstallation\n------------\n\nSomething like::\n\n $ pip install GenomeBaser\n\nAlternatively::\n\n $ wget https://github.com/mscook/GenomeBaser/archive/v0.1.2.tar.gz\n $ tar -zxvf v0.1.2.tar.gz\n $ cd v0.1.2\n $ # May need sudo/root, BUT...\n $ python setup.py install\n\n\nUsage\n-----\n\nSomething like::\n\n $ GenomeBaser --help\n Usage: GenomeBaser [OPTIONS] GENUS SPECIES OUT_DATABASE_LOCATION\n\n GenomeBaser is tool to manage complete (bacterial) genomes from the NCBI.\n\n Example usage:\n\n $ GenomeBaser.py Klebsiella pneumoniae ~/dbs\n\n $ # (wait a few months)...\n\n $ GenomeBaser Klebsiella pneumoniae ~/dbs\n\n By Mitchell Stanton-Cook (m.stantoncook@gmail.com)\n\n **More info at:** https://github.com/mscook/GenomeBaser\n\n Options:\n --check_deps / --no-check_deps Check that non-python dependencies exist\n --help Show this 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