<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif; "><div>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.</div><div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> Joe Wilders <<a href="mailto:joe.wilders@gmail.com">joe.wilders@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Mon, 19 Mar 2012 09:53:37 +0800<br><span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Cc: </span> <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> Re: [maker-devel] maker gff3 to genbank tbl/gbk<br></div><div><br></div><br>Hi Carson,<div>Thank you very much for your suggestion, will try that up and let you know.</div><div><br></div><div>by the way <span style="">i did found this in one of the revisions at the svn </span><a href="http://malachite.genetics.utah.edu/projects/maker/browser/bin/gff3_2_gbk?rev=217" target="_blank" style="">http://malachite.genetics.utah.edu/projects/maker/browser/bin/gff3_2_gbk?rev=217</a><span style=""> , i wonder why it gets pulled out on the later revision..</span></div><div><br></div><div><br><div class="gmail_quote">On Mon, Mar 19, 2012 at 6:21 AM, Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Try using Apollo. You can open up GFF3 files and them save them as<br>
GenBank format. That might be sufficient.<br><br>
Alternatively. I've attached a script that can convert SNAP's ZFF format<br>
to GeneBank. You could then use the maker2zff that comes with MAKER to<br>
convert results to ZFF and then this script to get GenBank format.<br><br>
Thanks,<br>
Carson<br><div class="HOEnZb"><div class="h5"><br>
On 12-03-14 1:31 AM, "Joe Wilders" <<a href="mailto:joe.wilders@gmail.com">joe.wilders@gmail.com</a>> wrote:<br><br>
>Dear MAKER experts,<br>
><br>
>i hope that you can share your expertise regarding, conversion of<br>
>maker gff3 to genbank tbl or gbk. im trying to produce a working<br>
>genbank tbl, i tried converting to chado using maker2chado and<br>
>gmodtools genbanksubmit writer. but so far it doesnt end well. most<br>>probably due to xml configuration(which im really loss, especially<br>
>defining the "goldenpath") .is there any other way to produce the tbl<br>
>from maker output?<br>
><br>
>thanks :)<br>
><br>
>Joe Wilders<br>
><br>
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