Brad Chapman

Yarden and Ryan; I'd be happy to contribute code and help with this. I'm agreed with all your points about GFF3 format peculiarities, and that a good first step is...

Sorry about the issue. If you're running into problems with the conversion script we'll need a bit more information to be able to diagnose: ideally the full error traceback, the...

Bobby; That would be great. I wish the spec had a more consistent and standard quoting approach instead of something custom, hence my use of urllib.quote/unquote. If it's causing issues...

Bobby; Thanks much for looking at this. I didn't see a patch in your reply. Could you send a pull request, or post the patch as a Gist? Thanks again.

Bobby; These e-mails come in as GitHub issue comments, and it looks like they remove attachments so I'm not getting it. You can see them on the issue page: https://github.com/chapmanb/bcbb/issues/86...

Francesco -- sorry about the issues. In general, we've been recommeding using the gffutils parser, which is nicer and more actively maintained: https://github.com/daler/gffutils. Would you be able to try this...

Eric; Sorry about the issue. Have you tried looking at parsing in gffutils (https://github.com/daler/gffutils)? It's a better representation of the approach used here and is well maintained by Ryan. I've...

Timothée; Thanks for the report and sorry to be slow in getting back with you. This script only handles formatting conversion -- taking what is in the GenBank file and...

Björn and Mikael; Sorry about leaving this for so long. I've been meaning to tackle it forever. Have you tried using GFFutils: https://github.com/daler/gffutils I've been pointing everyone at Ryan's work...

James -- thanks so much. This sounds promising although the bits about producing valid cram streams with dd is beyond my CRAM skill level, in terms of producing a proof...