nebgbhist Annotation histories from Genbank files.
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Python library histories annotation Genbank annotation histories

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Annotation histories from Genbank files. nebgbhist contains 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.gbkPlaying with filesIf 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 -1accession dblink keywords objects/ seq/ versioncomment definition locus ref/ sourceFiles 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.Developer commentsI recommend that you work with nebpack.Pack objects if you want to actually do anything with the objects. Requirements: · Python

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