<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>All maker gene annotations will be of the format gene/mRNA/exon/CDS. Anything in the format match/match_part is an evidence alignment or rejected model and is there for reference purposes. If you want to upgrade all of the rejected loci to gene annotations, set keep_preds=1 in the control files. If you want to upgrade a subset of rejected models to a full annotation, create a list of IDs (one per line) then give them to the attached script. gff3_preds2models was previously deprecated and no longer part of the maker distribution, but the attached script is an updated version with the same functionality. </div><div><br></div><div>--Carson</div><div><br></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> Innocent Onsongo <<a href="mailto:onson001@umn.edu">onson001@umn.edu</a>><br><span style="font-weight:bold">Date: </span> Wednesday, 5 June, 2013 12:35 PM<br><span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carson.holt@oicr.on.ca">carson.holt@oicr.on.ca</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>>, Barry Moore <<a href="mailto:barry.utah@gmail.com">barry.utah@gmail.com</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] Maker: accessory scripts<br></div><div><br></div><div dir="ltr">I was able to successfully ran Maker and now want to c<span style="color:rgb(0,0,0);font-family:sans-serif;font-size:13px;line-height:19px">onverts the gene prediction match/match_part format to annotation gene/mRNA/exon/CDS format. I looked at the tutorial and the script </span><span style="background-color: rgb(249, 249, 249); color: rgb(0, 0, 0); font-size: 13px; line-height: 19px; font-family: 'Lucida Console', Monaco, 'Courier New', Courier, monospace; ">gff3_preds2models</span><div style=""><span style="color:rgb(0,0,0);font-family:sans-serif;font-size:13px;line-height:19px">is supposed to do this conversion. How do I access this script. It is not in </span>/maker/2.28-beta/bin/<br></div><div style=""><br></div><div style="">Also, in running <span style="background-color: rgb(249, 249, 249); color: rgb(0, 0, 0); font-size: 13px; line-height: 19px; font-family: 'Lucida Console', Monaco, 'Courier New', Courier, monospace; ">gff3_preds2models <gff3 file> <pred list> </span> is <<span style="background-color: rgb(249, 249, 249); color: rgb(0, 0, 0); font-size: 13px; line-height: 19px; font-family: 'Lucida Console', Monaco, 'Courier New', Courier, monospace; ">pred list> the file I used for </span><span style="background-color: rgb(249, 249, 249); color: rgb(0, 0, 0); font-size: 13px; line-height: 19px; font-family: 'Lucida Console', Monaco, 'Courier New', Courier, monospace; ">pred_gff=? </span></div><div style=""><span style="background-color: rgb(249, 249, 249); color: rgb(0, 0, 0); font-size: 13px; line-height: 19px; font-family: 'Lucida Console', Monaco, 'Courier New', Courier, monospace; "><br></span></div><div style="">Long story short, how do I transform the GFF output from Maker to the more traditional annotation of exon/intron? <br></div><div style=""><br></div><div style=""><span style="background-color: rgb(249, 249, 249); color: rgb(0, 0, 0); font-size: 13px; line-height: 19px; font-family: 'Lucida Console', Monaco, 'Courier New', Courier, monospace; ">Thanks, </span></div><div style="">Getiria</div></div>
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