--- a
+++ b/annotate_mouse_transcriptome.py
@@ -0,0 +1,29 @@
+import re
+in_genes="Mus_musculus.GRCm38.84.with_tid.gtf"
+out_genes="Mus_musculus.GRCm38.84.annotated.gtf"
+accepted_gene_biotypes_for_NA_transcripts = set(["IG_V_gene","IG_J_gene","protein_coding","TR_J_gene","TR_D_gene","TR_V_gene","IG_C_gene","IG_D_gene","TR_C_gene"])
+with open(in_genes, 'r') as in_f, open(out_genes, 'w') as out_f:
+    for line in in_f:
+        chr_name = line.rstrip().split('\t')[0]
+        # Check the transcript_support level
+        # This should be faster than a regex
+        # We need to support the case where see these two types of annotations:
+        #   transcript_support_level "1"
+        #   transcript_support_level "1 (assigned to previous version X)"
+        #   transcript_support_level "2" <- Clear example of a gene like this is NKX6.1
+        #   transcript_support_level "2 (assigned to previous version X)"
+        line_valid_for_output = False
+        if 'transcript_support_level "1"' in line or 'transcript_support_level "1 ' in line or 'transcript_support_level "2"' in line or 'transcript_support_level "2 ' in line:
+            line_valid_for_output = True
+        elif 'transcript_support_level "NA' in line:
+            # Transcript Support Level Not Analysed. Pseudogenes, single exon transcripts, HLA, T-cell receptor and Ig transcripts are not analysed and therefore not given any of the TSL categories.
+            # Keep only a few ones annotated as "IG_V_gene","IG_J_gene","protein_coding","TR_J_gene","TR_D_gene","TR_V_gene","IG_C_gene","IG_D_gene","TR_C_gene"
+            gene_biotype = re.search(r'gene_biotype \"(.*?)\";', line)
+            if gene_biotype and gene_biotype.group(1) in accepted_gene_biotypes_for_NA_transcripts:
+                line_valid_for_output = True
+        if line_valid_for_output:
+            gene_name = re.search(r'gene_name \"(.*?)\";', line)
+            if gene_name:
+                gene_name = gene_name.group(1)
+                out_line = re.sub(r'(?<=transcript_id ")(.*?)(?=";)', r'\1|'+gene_name, line)
+                out_f.write(out_line)
\ No newline at end of file