--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cpt_trnascanse_to_gff/tRNAscan_to_gff_SE_format.py	Fri May 13 18:03:32 2022 +0000
@@ -0,0 +1,38 @@
+#!/usr/bin/env python
+import fileinput
+
+print ("##gff-version-3")
+# process each trna in tsv file
+metaLines = 0
+for trna in fileinput.input():
+    if metaLines < 3:
+      metaLines += 1
+      continue
+    cols_tsv = trna.split("\t")
+    if int(cols_tsv[2]) < int(cols_tsv[3]):
+      cols_gff = [
+        cols_tsv[0].strip(),
+        "tRNAscan",
+        "tRNA",
+        cols_tsv[2].strip(),
+        cols_tsv[3].strip(),
+        cols_tsv[8],
+        "+",
+        ".",
+        'ID=trna.%s;Anticodon=%s;Codon=tRNA-%s'
+        % (cols_tsv[1], cols_tsv[5].lower(), cols_tsv[4]),
+      ]
+    else:
+      cols_gff = [
+        cols_tsv[0].strip(),
+        "tRNAscan",
+        "tRNA",
+        cols_tsv[3].strip(),
+        cols_tsv[2].strip(),
+        cols_tsv[8],
+        "-",
+        ".",
+        'ID=trna.%s;Anticodon=%s;Codon=tRNA-%s'
+        % (cols_tsv[1], cols_tsv[5].lower(), cols_tsv[4]),
+      ] 
+    print ("\t".join(cols_gff))