Question

Is there a genbank format validator out there?

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8.5 years ago

bitjunkie ▴ 40

Does anyone have a script that can validate the feature table in genbank files against the format specification by INSDC found here?

Also, I only need it for bacterial genomes, plasmids.

genbank • 3.1k views

ADD COMMENT • link updated 20 months ago by Ram 43k • written 8.5 years ago by bitjunkie ▴ 40

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Entering edit mode

Thanks Chris. The feature table is what I'm interested in -- I don't care about the rest of the file. Edited my question as such.

ADD REPLY • link updated 4.4 years ago by Ram 43k • written 8.4 years ago by bitjunkie ▴ 40

Ram · Answer 1 · 2015-11-13

That is a description of the feature table format, which is part of a GenBank file; it could be validated on its own. However, there isn't a specification for 'GenBank format' as a whole as far as I know; without that it's hard to validate (an example file exists but definitely can't be used for validation as it covers a single case and doesn't deal with variations such as WGS assembly master records).