semvec/pypi-packages huggingface dataset:
nebgbhist 0.0.5
Annotation histories from Genbank files.
License: MIT
Keywords: bioinformatics Genbank annotation history

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.