Metadata-Version: 1.0
Name: nebgbhist
Version: 0.0.5
Summary: Annotation histories from Genbank files.
Home-page: http://github.com/davisp/nebgbhist
Author: Paul Joseph Davis
Author-email: davisp@neb.com
License: MIT
Description: nebgbhist
        =========
        
        Tools for building annotation histories from multiple Genbank files.
        
        Example
        =======
        
        ::
        
        $ mkdir gbhist
        $ neb-rev-fetch -d gbhist NC_008512
        $ neb-gbhist -d gbhist | neb-diff-apply NC_008512.git
        $ git --git-dir=NC_008512.git gc --aggressive
        $ neb-validate-history -p NC_008512.git -g gbhist/2009-04-29-04-04.gbk
        
        Playing with files
        ==================
        
        If you clone the pack repository after building you can poke around at the
        contents on the file system. For larger genomes with lots of edits this may run
        afoul of directory entry limits until I rewrite the object storage. For the
        Carsonella (NC_008512) example I use there isn't an issue.
        
        ::
        
        $ git clone NC_008512.git
        $ cd NC_008512
        $ ls -1
        accession  dblink     keywords   objects/   seq/       version
        comment    definition locus      ref/       source
        
        Files in the root directory represent keywords defined in the Genbank file. The
        ref and seq subdirectories contain information about references and the sequence
        hashes. The objects directory lists the features in the history. The files
        objects/known and objects/alive are dictionaries of hashes that point toward
        the current version of a feature at a given location. Active features are
        anything that is not deleted or replaced with a new version.
        
        I recommend that you work with nebpack.Pack objects if you want to actually do
        anything with the objects.
        
        
Keywords: bioinformatics Genbank annotation history
Platform: any
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Software Development :: Libraries :: Python Modules
