[maker-devel] Problem with cegma2zff

[David Powell]

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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