Add get_num_of_exons.py

workflow/scripts/get_num_of_exons.py

@@ -0,0 +1,38 @@
+"""
+Dogukan Bayraktar
+Python Version 3.10
+Gets number of exons per transcript from a GTF file
+"""
+
+from collections import defaultdict
+from argparse import ArgumentParser
+
+parser = ArgumentParser(description='Gets number of exons per transcript from a GTF file')
+parser.add_argument('--GTF', type=str,  help='Full path to GTF file')
+parser.add_argument('--output', type=str, help='Name of the output file')
+args = parser.parse_args()
+
+if __name__ == "__main__":
+
+    transcripts = defaultdict(int)
+    with open(args.GTF, "r") as content:
+        for line in content:
+            if line.startswith("#"):
+                continue
+            line = line.split()
+            feature = line[2]
+            if feature == "exon":
+                transcript_id = line[13][1:-2]
+                transcripts[transcript_id] += 1
+
+    exons = defaultdict(int)
+    for num_exons in transcripts.values():
+        exons[num_exons] += 1
+
+    with open(args.output, "w") as outfile:
+        outfile.write(f'Transcript_exon_length\tNumber_of_transcripts\n')
+        sorted_exons = sorted(exons.items())
+        for item in sorted_exons:
+            num_exon = item[0]
+            count = item[1]
+            outfile.write(f'{num_exon}\t{count}\n')