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--- modifygffforclc_gw.pl [2017/01/24 11:36] – hyjeong
+++ modifygffforclc_gw.pl [2021/03/17 13:09] (current) – external edit 127.0.0.1
@@ Line 1: / Line 1: @@
+  #!/usr/bin/perl
+  #
+  # This script assumes that the input GFF file has only CDS/tRNA/rRNA/tmRNA
+  # features. It adds gene features to all of them, and also adds "mRNA" features
+  # to each CDSs.
+  #
+  #
+  while (<>) {
+    chomp;
+    print $_, "\n" if /^#/;
+    last if /^##FASTA/ || /^>/;
+    my @data = split /\t/, $_;
+    if ($data[2] =~ /(CDS|rRNA|tRNA|tmRNA)/) {  # skip e.g. repeat_region
+        $type = $1;
+        $data[2] = 'gene';
+        print join "\t", @data; print "\n";     # add gene feature
+        if ($type eq 'CDS') {
+            $data[2] = 'mRNA';
+            print join "\t", @data; print "\n";
+        }
+    }
+    print $_, "\n";   # print the original line
+  }