Convert GFF file to Sequin TBL file

[sjackman]

Submitting to GenBank requires converting a GFF file to a Sequin TBL file, which is then converted ASN.1 using tbl2asn. I have searched, and I have not found a good (or any, really) converter from GFF to Sequin TBL. Would you be interested in adding such a tool? Here's the hacky script that I cobbled together for this purpose: gff3-to-tbl. It's not general purpose, but could be a useful starting point.

[chapmanb]

Shaun;
Definitely, happy to pull this into the gff scripts directory if you want to submit a pull request. Thanks for making it available.

For a suggestion that requires more work, have you thought about migrating it to gffutils (https://github.com/daler/gffutils) and pushing it upstream there? I've generally been pointing people at that rather than this implementation. Ryan did an awesome job with it and it's more scalable than my implementation.

[sjackman]

@daler Would you like a GFF to Sequin TBL converter in gffutils? See above.

[sjackman]

This task isn't a regular task of mine, so the maintenance burden would largely fall on the shoulder's of whomever adopted it. I'd love for this script to find a permanent home though. It's really odd that a good GFF to Sequin TBL converter doesn't already exist, but I wasn't able to find one.

[daler]

Hi Shaun -

It looks like it can be readily ported to gffutils. I've been meaning to have a collection of conversion scripts (like creating refFlat files from GTF or GFF files), but don't have anything started yet. A gffutils.conversion module would be a good home for this GFF to TBL script.

I'm unfamiliar with the TBL format though. If you could submit a pull request to gffutils with some example input/output, some basic functional tests, and the existing script, I can do the porting to gffutils.

[sjackman]

Hi, Ryan. Here are two genomes that I annotated in GFF and converted to TBL format using this script. They have some fun trans-splicing and RNA editing exceptions.

1. GFF and TBL
2. GFF and TBL

[sjackman]

Here's a description of the Sequin TBL format:

1. http://www.ncbi.nlm.nih.gov/projects/Sequin/table.html
2. http://www.ncbi.nlm.nih.gov/genbank/genomesubmit_annotation

[sjackman]

NCBI now accepts submissions to GenBank in GFF3 format, so the original use case for this request exists no longer. See https://www.ncbi.nlm.nih.gov/genbank/genomes_gff/

[chapmanb]

Shaun;
Thanks for following up. I've been pointing everyone at gffutils for GFF work since I haven't worked on this in a while, but glad this just magically went away 3 years later.

[sjackman]

Motivational poster:

Procrastination

Why do today that which will be unnecessary tomorrow?

[SLAment]

I should add that your script @sjackman is still useful in case you happen to have a small gff for small contigs that you want to submit through BankIt. In that case, as far as I can tell, you still need the tbl file.

[sjackman]

My workflow is still converting my GFF files to TBL using this script, and using the normal tbl2asn rather than the GFF version.