<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>Some of your iprscan results contain truncated names</div><div><br></div><div>Example:</div><div>maker-NODE_5172_length_118591_cov_102.277115-snap-gene-0.100-mR</div><div><br></div><div>This seems to be the case for almost all HMMPanther and HMMSmart results.</div><div><br></div><div>Try just removing those two groups of results from your file for now.</div><div><br></div><div>Then use the iprscan_wrap script that comes with maker to just re-run just those two application within iprscan it will fix the truncation issue (it creates temporary short names and then converts back to the longer names when it parses the results).</div><div><br></div><div>Thanks,</div><div>Carson</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> Fourie Joubert <<a href="mailto:fourie.joubert@up.ac.za">fourie.joubert@up.ac.za</a>><br><span style="font-weight:bold">Date: </span> Friday, 21 September, 2012 9:58 AM<br><span style="font-weight:bold">To: </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> [maker-devel] Problems parsing iprscan results with iprscan2gff3<br></div><div><br></div><div>
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Hi Folks<br>
<br>
I am running into some problems parsing iprscan results.<br>
<br>
I run iprscan as follows:<br>
<br>
<font face="Calibri,Verdana,Helvetica,Arial"><span style="font-size:11pt">> iprscan -cli -i
bot.all.maker.proteins.fasta -o bot.all.maker.proteins.raw
-format raw -goterms -iprlookup</span></font><br>
<br>
and obtain the iprscan output (the iprscan output file is at
<a class="moz-txt-link-freetext" href="http://www.bi.up.ac.za/~fourie/bot.all.maker.proteins.raw">http://www.bi.up.ac.za/~fourie/bot.all.maker.proteins.raw</a> if anyone
is interested in the detailed output, and the initial maker gff3
file is at <a class="moz-txt-link-freetext" href="http://www.bi.up.ac.za/~fourie/bot.all.gff">http://www.bi.up.ac.za/~fourie/bot.all.gff</a>).<br>
<br>
I then try to run the conversion to gff3, but I get very long list
of errors:<br>
<font face="Calibri,Verdana,Helvetica,Arial"><span style="font-size:11pt"><br>
> iprscan2gff3 bot.all.maker.proteins.raw bot.all.gff > domains.gff</span></font><br>
<br>
ERROR: In
maker-NODE_4797_length_138874_cov_96.632576-augustus-gene-0.113<br>
Use of uninitialized value $seqid in concatenation (.) or string at
/usr/local/maker/bin/iprscan2gff3 line 255.<br>
Use of uninitialized value $start in concatenation (.) or string at
/usr/local/maker/bin/iprscan2gff3 line 255.<br>
Use of uninitialized value $end in concatenation (.) or string at
/usr/local/maker/bin/iprscan2gff3 line 255.<br>
Use of uninitialized value $strand in concatenation (.) or string at
/usr/local/maker/bin/iprscan2gff3 line 255.<br>
Use of uninitialized value $off in subtraction (-) at
/usr/local/maker/bin/iprscan2gff3 line 267.<br>
Use of uninitialized value $pB in subtraction (-) at
/usr/local/maker/bin/iprscan2gff3 line 267.<br>
Use of uninitialized value $off in subtraction (-) at
/usr/local/maker/bin/iprscan2gff3 line 267.<br>
Use of uninitialized value $pE in subtraction (-) at
/usr/local/maker/bin/iprscan2gff3 line 267.<br>
Use of uninitialized value $seqid in concatenation (.) or string at
/usr/local/maker/bin/iprscan2gff3 line 269.<br>
Use of uninitialized value $start in concatenation (.) or string at
/usr/local/maker/bin/iprscan2gff3 line 269.<br>
Use of uninitialized value $end in concatenation (.) or string at
/usr/local/maker/bin/iprscan2gff3 line 269.<br>
Use of uninitialized value $strand in concatenation (.) or string at
/usr/local/maker/bin/iprscan2gff3 line 269.<br>
.......<br>
.......<br>
.......<br>
<br>
for most of the entries.<br>
<br>
Any advice or help would be sincerely appreciated!<br>
<br>
Best regards!<br>
<br>
Fourie<br>
<br>
<br>
<br>
<pre class="moz-signature" cols="72">--
--------------
Prof Fourie Joubert
Bioinformatics and Computational Biology Unit
Department of Biochemistry
University of Pretoria
<a class="moz-txt-link-abbreviated" href="mailto:fourie.joubert@up.ac.za">fourie.joubert@up.ac.za</a><a class="moz-txt-link-freetext" href="http://www.bi.up.ac.za">http://www.bi.up.ac.za</a>
Tel. +27-12-420-5825
Fax. +27-12-420-5800
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