[maker-devel] maker gff3 to genbank tbl/gbk

[Carson Holt]

A lot of the early code in the SVN suppository, contains one-off scripts.
This one looks a lot like one of my old scripts.  If I remember, I was
trying to get GenBank format for Augustus training.  I started with just a
quick BioPerl based conversion, but the script didn't produce the right
types in GenBank format.  I found another way to do what I wanted (i.e.
someone gave me a different script that worked well enough), and I just
abandoned that script.

Thanks,
Carson


From:  Joe Wilders <joe.wilders at gmail.com>
Date:  Mon, 19 Mar 2012 09:53:37 +0800
To:  Carson Holt <carsonhh at gmail.com>
Cc:  <maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] maker gff3 to genbank tbl/gbk


Hi Carson,
Thank you very much for your suggestion, will try that up and let you know.

by the way i did found this in one of the revisions at the svn
http://malachite.genetics.utah.edu/projects/maker/browser/bin/gff3_2_gbk?rev
=217 , i wonder why it gets pulled out on the later revision..


On Mon, Mar 19, 2012 at 6:21 AM, Carson Holt <carsonhh at gmail.com> wrote:
> Try using Apollo.  You can open up GFF3 files and them save them as
> GenBank format.  That might be sufficient.
> 
> Alternatively.  I've attached a script that can convert SNAP's ZFF format
> to GeneBank.  You could then use the maker2zff that comes with MAKER to
> convert results to ZFF and then this script to get GenBank format.
> 
> Thanks,
> Carson
> 
> On 12-03-14 1:31 AM, "Joe Wilders" <joe.wilders at gmail.com> wrote:
> 
>> >Dear MAKER experts,
>> >
>> >i hope that you can share your expertise regarding, conversion of
>> >maker gff3 to genbank tbl or gbk. im trying to produce a working
>> >genbank tbl, i tried converting to chado using maker2chado and
>> >gmodtools genbanksubmit writer. but so far it doesnt end well. most
>> >probably due to xml configuration(which im really loss, especially
>> >defining the "goldenpath") .is there any other way to produce the tbl
>> >from maker output?
>> >
>> >thanks :)
>> >
>> >Joe Wilders
>> >
>> >_______________________________________________
>> >maker-devel mailing list
>> >maker-devel at box290.bluehost.com
>> >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> 



-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20120319/b21d586b/attachment-0003.html>