<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); "><div style="font-family: Calibri, sans-serif; font-size: 14px; ">Sorry for the slow response. The <span class="Apple-style-span" style="font-size: 15px; font-family: Calibri; ">gff3_preds2models script has been deprecated for some time now (isn't even in the release code anymore), and the old one won't work with the new library.</span></div><div style="font-family: Calibri, sans-serif; font-size: 14px; "><span class="Apple-style-span" style="font-size: 15px; font-family: Calibri; "><br></span></div><div style="font-family: Calibri, sans-serif; font-size: 14px; "><span class="Apple-style-span" style="font-size: 15px; font-family: Calibri; ">I've attached a made from scratch drop-in replacement that you can use to do what the old script would have done. In the current release of MAKER, instead of the gff3_preds2models script users can just give MAKER a set of predictions in GFF3 format (pred_gff option) and set keep_preds=1 (then leave all other options blank). The predictions given will the be converted into gene models.</span></div><div style="font-family: Calibri, sans-serif; font-size: 14px; "><span class="Apple-style-span" style="font-size: 15px; font-family: Calibri; "><br></span></div><div><span class="Apple-style-span" style="font-size: 15px;">Thanks,</span></div><div><span class="Apple-style-span" style="font-size: 15px;">Carson</span></div><div><span class="Apple-style-span" style="font-size: 15px;"><br></span></div><div><span class="Apple-style-span" style="font-size: 15px;"><br></span></div><div style="font-family: Calibri, sans-serif; font-size: 14px; "><br></div><span id="OLK_SRC_BODY_SECTION" style="font-size: 14px; font-family: Calibri, sans-serif; "><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> Walter Eckalbar <<a href="mailto:weckalba@asu.edu">weckalba@asu.edu</a>><br><span style="font-weight:bold">Date: </span> Tuesday, 3 April, 2012 7:28 PM<br><span style="font-weight:bold">To: </span> <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] gff3_preds2models usage question<br></div><div><br></div>Hello maker developers and users,<div><br></div><div><span class="Apple-style-span">I am attempting to use the gff3</span>_preds2models<span class="Apple-style-span"> scripts, but running into a few issues.</span></div><div><br></div><div>Initially, I hit errors that seemed to be fixed by installing CGI and its dependancies. However, that during that installation a few tests did fail. I can provide error logs if that would be helpful, however, I went on to install and attempt gff3_preds2models anyway.</div><div><br></div><div>What I am currently doing is running gff3_merge first, to gather the maker outputs. I am doing so with both the -n option on and off. When providing the gff3 file with the sequence I get the following error from gff3_preds2models:</div><div><br></div><div>Undefined subroutine &maker::auto_annotator::annotate called at /Users/Walter/Bioinformatics/Tools/maker/bin/gff3_preds2models line 97, <GEN16> line 992291.</div><div><br></div><div>This seemed to be the same error as that of what someone else saw on these boards, but I did not see a later email resolving the issue.</div><div><br></div><div>I also tried giving it just the gff3 without the sequences at the bottom of the file and then I get this error:</div><div><br></div><div><div>ERROR: There was a problem in the writing the fasta entry</div><div>Either no sequence was given, or there was an error in writing</div></div><div><br></div><div>This leads me to believe I should be using the one with the sequence, but I am not certain of that.</div><div><br></div><div>
I see it might be possible to go from maker outputs to chado database then to gene->mRNA->exon gff3s, but I have not set up my machine for XML or chado yet, and it does not appear trivial.</div><div><br></div><div>Thanks for the help,</div><div><br></div><div>Walter</div>
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