<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>Also make sure there are gene/mRNA features in your GFF3 for your iprscan results. If you used the ab initio calls (which will be match/match_part features in the GFF3) as your input to iprscan, then you will need to upgrade them to gene/mRNA features before the script will add domains to them.</div><div><br></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> Daniel Ence <<a href="mailto:dence@genetics.utah.edu">dence@genetics.utah.edu</a>><br><span style="font-weight:bold">Date: </span> Thursday, June 19, 2014 at 2:44 PM<br><span style="font-weight:bold">To: </span> Rebecca Harris <<a href="mailto:rbharris@uw.edu">rbharris@uw.edu</a>><br><span style="font-weight:bold">Cc: </span> "<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>" <<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] Fwd: iprscan2gff3<br></div><div><br></div><div><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">
Hi Rebecca, I at the conversation you linked to and it seems that Carson resolved the those parsing issues in an update to maker. What version of maker are you using?
<div><br></div><div>Also, in that same conversation Carson said that those errors wouldn't affect the output (because the script was parsing the mRNA features fine, but giving errors on the gene features). Does the output that you get from iprscan2gff3 seem complete?</div><div><br></div><div>~Daniel</div><div><br></div><div><br><div><div><div apple-content-edited="true"><div><span style="font-family: Tahoma; font-size: small; ">Daniel Ence</span></div><div><span style="font-family: Tahoma; font-size: small; ">Graduate Student</span></div><div><a href="mailto:dence@genetics.utah.edu">dence@genetics.utah.edu</a><br style="font-family: Tahoma; font-size: small; "><span style="font-family: Tahoma; font-size: small; ">Eccles Institute of Human Genetics</span><br style="font-family: Tahoma; font-size: small; "><span style="font-family: Tahoma; font-size: small; ">University of Utah</span><br style="font-family: Tahoma; font-size: small; "><span style="font-family: Tahoma; font-size: small; ">15 North 2030 East, Room 2100</span><br style="font-family: Tahoma; font-size: small; "><span style="font-family: Tahoma; font-size: small; ">Salt Lake City, UT 84112-5330</span></div></div><br><div><div>On Jun 19, 2014, at 1:07 PM, Rebecca Harris <<a href="mailto:rbharris@uw.edu">rbharris@uw.edu</a>></div><div> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div dir="ltr"><div class="gmail_quote"><div dir="ltr">Hi,
<div><br></div><div>I'm trying to use the iprscan2gff3 script to update my final gff3 file with annotations from Interproscan 5. I'm getting a bunch of errors similar to another user but do not see how their issue was resolved: </div><div><a href="https://groups.google.com/forum/#!searchin/maker-devel/iprscan2gff3/maker-devel/MykTxL2Da64/5yrO3e6WBHUJ" target="_blank">https://groups.google.com/forum/#!searchin/maker-devel/iprscan2gff3/maker-devel/MykTxL2Da64/5yrO3e6WBHUJ</a></div><div><br></div><div>I ran Interproscan on my ab initio predictions, then converted the xml to raw format. When I run iprscan2gff3 I get the errors: </div><div><p>Use of uninitialized value $name in hash element at /gscratch/leache/rbharris/maker/bin/ipr_update_gff line 107, <$IN> line 1090.</p></div><div>Thanks,</div><div>Rebecca</div></div></div><br></div>
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