GenBank to .tbl (Sequin format)

[ErinL]

Hi everyone,

I'm working on submitting a set of whole genome shotgun sequencing projects to GenBank/NCBI. For this set of genomes, I have annotations which were generated using the RAST system (in GenBank and FFF format). However, in order to submit to GenBank/NCBI, these annotations need to be converted to what NCBI calls a 'feature table' (Sequin format/.tbl file). The file format is detailed here: http://www.ncbi.nlm.nih.gov/Sequin/table.html

I've searched the web for parsers to create the required table format using either GenBank or FFF formated files, and have asked the NCBI support staff if they know of such a parser. However, I have not been able to find one. Does anyone know where I can find something to convert between GenBank or FFF and the NCBI feature table format?

Thanks in advance!

Sincerely,
Erin

[maubp]

I thought you could give them GenBank/EMBL files too? Maybe I'm thinking of EMBL not the NCBI...

P.S. What is this "FFF format"? I thought it was a typo for GFF, but you did it three times.

[nickloman]

I thought you could give them GenBank/EMBL files too? Maybe I'm thinking of EMBL not the NCBI...

Unfortunately not Bit crazy. But it's easy to write a conversion script between the two. I've got one somewhere.

[ErinL]

I asked and they won't except GenBank files. It seems a bit crazy, since that's what they're going to make out of the .tbl/Sequin file anyway.

I'm sure I could write my own conversion script, but I'm a bit new to this whole scripting business, so it may take me a whole. I thought it was worth checking with the community to see if someone had one handy before I go through the trouble.

And yes, FFF was a typo for GFF. Guess my thinking cap was a bit loose at the end of the day. Sorry for the confusion.

[ErinL]

Just found one parser that claims to convert between GenBank and Sequin, but it appears to work for only one contig at a time (created table ends after the last gene of the first contig) and ignores tRNAs.

http://lfz.corefacility.ca/gbk2tbl/

[nickloman]

I'll try and dig out my script.

If it's any help, Torsten Seemann's automated annotation pipeline can output sequin and/or table format:

http://bioinformatics.net.au/prokka-manual.html

[ErinL]

Thanks nickloman, we've thought about just re-doing the annotations through NCBI's pipeline, but the problem is we already used the annotations we have for all of our analyses and want to have them associated with the genomes when we submit them. I'm working on seeing if I can use the parser I posted above if I pre-split the files into contigs and add the tRNAs/rRNAs by hand, but I'll keep an eye out in case you find your script first!

[nickloman]

Found it! Hope it's vaguely useful:

https://gist.github.com/2660685

[ErinL]

Great! Thanks!

Erin

[ErinL]

Hey nikloman,

Just as an fyi and a note for potential future users of your script, the code you linked to broke at the first CDS feature in my GBK. I made a couple of minor changes and it seems to work now, although it doesn't pick up the annotations for the tRNAs/rRNAs. At this point I figure it's relatively trivial to go through and add those in by hand for a small number of genomes. In the future I will be submitting an additional ~70 genomes, and will (hopefully) post an updated script with that feature fixed.

I've attached my edits as a plain text file (the forum wont accept a .py file).

Thank you again!

Erin

[nickloman]

Ah OK, well it's like most scripts - you get it working for your problem and then you forget about it. But glad you could make it run for you!

[oudacontrol]

Have either of you found a gff to the Sequin format/.tbl file converter?

[ErinL]

Have either of you found a gff to the Sequin format/.tbl file converter?

nickloman's script works fine for the format conversion itself, but then there are a myriad of changes that must be made to your original annotations to conform with GenBank naming conventions. For the number of genomes I'm submitting, I found it easier to just submit the fasta files for re-submission through NCBI's pipeline, which spits out Sequin formatted files.

[seb.lees]

Hi everyone.

for people who have Artemis intalled on their computer, you can also open the .gbk with the soft and use the 'SAVE AS' menu to save it under the sequin/tbl format.

All features are kept, as well as tRNA and rRNA information.

hope it may help.

seb.

[wanyu]

Thanks, it helps me, but Artemis can only read and convert the first contig in a muti-genbank file.

Hi everyone.

for people who have Artemis intalled on their computer, you can also open the .gbk with the soft and use the 'SAVE AS' menu to save it under the sequin/tbl format.

All features are kept, as well as tRNA and rRNA information.

hope it may help.

seb.