[maker-devel] Problem with cegma2zff

[Carson Holt]

Yes.  There was an update for CEGMA that causes features to be duplicated in
it's output.  Thanks for the post and the fix.

--Carson


From:  David Powell <david.powell at monash.edu>
Date:  Thursday, 6 September, 2012 8:23 PM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Problem with cegma2zff

Greetings,

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.

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).

Just wanted to post this here in case this fix is useful to anyone else.

Cheers,

-- David Powell

diff --git a/cegma2zff b/cegma2zff
index c795da8..a3bbb77 100755
--- a/cegma2zff
+++ b/cegma2zff
@@ -39,6 +39,8 @@ while(my $line = <IN>){
     my @F = split("\t", $line);
     ($F[3], $F[4]) = ($F[4], $F[3]) if($F[6] eq '-');
 
+    next if $F[2] =~ /Exon/;
+
     $F[2] =~ s/First/Einit/;
     $F[2] =~ s/Terminal/Eterm/;
     $F[2] =~ s/Internal/Exon/;

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