20251125

99.scripts/trinity_utils/util/misc/frag_to_bed.pl

@@ -0,0 +1,32 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+use FindBin;
+
+use lib ("$ENV{EUK_MODULES}");
+use Gene_obj;
+
+
+while (<>) {
+    chomp;
+    my ($scaff, $read_acc, $lend, $rend) = split(/\t/);
+    
+    my $gene_obj = new Gene_obj();
+    $gene_obj->populate_gene_object({}, {$lend => $rend});
+    $gene_obj->{asmbl_id} = $scaff;
+    
+    $gene_obj->{TU_feat_name} = $read_acc;
+    $gene_obj->{Model_feat_name} = $read_acc;
+
+
+    print $gene_obj->to_BED_format();
+
+    
+    
+}
+
+exit(0);
+
+
+