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added a script to fix maker GFF so it can be loaded by PASA annotatio…

…n -- note still have to fix the alt-splicing exons problem
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commit 1e9161b87ac0a2dff94cf661a63c4247086a5ab0 1 parent 95860c1
@hyphaltip authored
Showing with 13 additions and 0 deletions.
  1. +13 −0 gene_prediction/fixmakergff_for_PASAannot.pl
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13 gene_prediction/fixmakergff_for_PASAannot.pl
@@ -0,0 +1,13 @@
+my $cds = 1;
+my $utr3 = 1;
+my $utr5 = 1;
+while(<>) {
+ if( s/:cds;Parent=/:cds:$cds;Parent=/ ) {
+ $cds++;
+ } elsif( s/:three_prime_utr;Parent=/:three_prime_utr:$utr3;Parent=/ ) {
+ $utr3++;
+ } elsif( s/:five_prime_utr;Parent=/:five_prime_utr:$utr3;Parent=/ ) {
+ $utr5++;
+ }
+ print;
+}
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