<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>Yes. There was an update for CEGMA that causes features to be duplicated in it's output. Thanks for the post and the fix.</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> David Powell <<a href="mailto:david.powell@monash.edu">david.powell@monash.edu</a>><br><span style="font-weight:bold">Date: </span> Thursday, 6 September, 2012 8:23 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] Problem with cegma2zff<br></div><div><br></div><div>Greetings,</div><div><br></div><div>I am using CEGMA to train SNAP for use with maker. However, I had a problem with the cegma2zff script that comes with maker. This script converts the gff file from CEGMA into a zff file for SNAP. </div><div><br></div><div>The problem is that it was producing a zff file with every multi-exon gene as being "invalid" from SNAPs point of view. My fix was to modify cegma2zff to ignore any feature with the tag "Exon" - as these are always duplicated by cegma as another feature (one of First, Internal, Terminal, Single).</div><div><br></div><div>Just wanted to post this here in case this fix is useful to anyone else.</div><div><br></div><div>Cheers,</div><div><br></div><div>-- David Powell</div><div><br></div><div><div>diff --git a/cegma2zff b/cegma2zff</div><div>index c795da8..a3bbb77 100755</div><div>--- a/cegma2zff</div><div>+++ b/cegma2zff</div><div>@@ -39,6 +39,8 @@ while(my $line = <IN>){</div><div> my @F = split("\t", $line);</div><div> ($F[3], $F[4]) = ($F[4], $F[3]) if($F[6] eq '-');</div><div> </div><div>+ next if $F[2] =~ /Exon/;</div><div>+</div><div> $F[2] =~ s/First/Einit/;</div><div> $F[2] =~ s/Terminal/Eterm/;</div><div> $F[2] =~ s/Internal/Exon/;</div></div><div><br></div>
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