{ "info": { "author": "Paul Joseph Davis", "author_email": "davisp@neb.com", "bugtrack_url": null, "classifiers": [ "Development Status :: 3 - Alpha", "Intended Audience :: Developers", "Intended Audience :: Science/Research", "License :: OSI Approved :: MIT License", "Natural Language :: English", "Operating System :: OS Independent", "Programming Language :: Python", "Topic :: Scientific/Engineering :: Bio-Informatics", "Topic :: Software Development :: Libraries :: Python Modules" ], "description": "nebgbhist\n=========\n\nTools for building annotation histories from multiple Genbank files.\n\nExample\n=======\n\n::\n\n $ mkdir gbhist\n $ neb-rev-fetch -d gbhist NC_008512\n $ neb-gbhist -d gbhist | neb-diff-apply NC_008512.git\n $ git --git-dir=NC_008512.git gc --aggressive\n $ neb-validate-history -p NC_008512.git -g gbhist/2009-04-29-04-04.gbk\n\nPlaying with files\n==================\n\nIf you clone the pack repository after building you can poke around at the\ncontents on the file system. For larger genomes with lots of edits this may run\nafoul of directory entry limits until I rewrite the object storage. For the\nCarsonella (NC_008512) example I use there isn't an issue.\n\n::\n\n $ git clone NC_008512.git\n $ cd NC_008512\n $ ls -1\n accession dblink keywords objects/ seq/ version\n comment definition locus ref/ source\n\nFiles in the root directory represent keywords defined in the Genbank file. The\nref and seq subdirectories contain information about references and the sequence\nhashes. The objects directory lists the features in the history. The files\nobjects/known and objects/alive are dictionaries of hashes that point toward\nthe current version of a feature at a given location. 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