[kproxy]

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

I was just wondering if you've updated this script to catch the tRNAs/rRNAs. I have been working in Artemis for dealing with my genomes but now would like to submit my 10 genomes with my annotations to genbank and have found no good way to generate the .tbl file.

Thanks!

[wanyu]

Hi,

I have done an edition of the script for converting a GenBank file into a Sequin feature table, which is based on the scripts by nickloman and ErinL. It worked well for me and my submission to GenBank was accepted.

gbk2tbl.py

Please let me know if you encounter any problem of using it.

Thanks.

I was just wondering if you've updated this script to catch the tRNAs/rRNAs. I have been working in Artemis for dealing with my genomes but now would like to submit my 10 genomes with my annotations to genbank and have found no good way to generate the .tbl file.

Thanks!

[Bioinform]

Hi Wanyu,

i get the following error.

pythogn gbk2tbl.py --modifiers modifier.txt PST.gbk

gbk2tbl.py: error: unrecognized arguments: PST.gbk

Thanks

[GenoMax]

Hi Wanyu,

i get the following error.

pythogn gbk2tbl.py --modifiers modifier.txt PST.gbk

gbk2tbl.py: error: unrecognized arguments: PST.gbk

Thanks

From GitHub page:

Usage: python gbk2tbl.py --mincontigsize 200 --prefix <prefix> --modifiers <modifier file> < annotation.gbk 2> stderr.txt

Your command should be

$ python gbk2tbl.py --modifiers modifier.txt < PST.gbk 2> stderr.txt

[wanyu]

From GitHub page:


Your command should be

$ python gbk2tbl.py --modifiers modifier.txt < PST.gbk 2> stderr.txt

Yes, you are right because the script takes both STDIN and arguments as inputs. I have changed the description of my script on GitHub to make it clearer.

[wanyu]

Hi Wanyu,

i get the following error.

pythogn gbk2tbl.py --modifiers modifier.txt PST.gbk

gbk2tbl.py: error: unrecognized arguments: PST.gbk

Thanks

Please use: python gbk2tbl.py --modifiers modifier.txt < PST.gbk, which means that the script reads the GenBank file from the standard input.

[iqra]

convert the gff3 file from ensembl into 'feature table' (Sequin format/.tbl file).?

i want to run this command .but i dont know how to get /make input file for this command
$ python gbk2tbl.py --modifiers modifier.txt < PST.gbk 2> stderr.txt