Deep Learning Workshop

@@ -86,7 +86,8 @@ if __name__ == "__main__":
         for row in reader:
             # print(row)
             filename = os.path.join(args.fastaPath, "Homo_sapiens.GRCh38.dna.chromosome.{}.fa".format(row['seqname']))
-            # We use only
+            if row['feature'] in ["exon", "five_prime_utr", "three_prime_utr"]:
+                # We use only exon, five_prime_utr, and three_prime_utr
                 sequence = get_sequence(filename, int(row['start']), int(row['end']))
                 # Features in HGA:
                 # exon
@@ -115,6 +116,7 @@ if __name__ == "__main__":
                 print("{} rows processed.".format(i))
             if i == 10000:
                 break
+    print("Count exons {} and utr {}".format(total_exon, total_utr))
     print("Length media exons {} and utr {}".format(length_total_exon/total_exon, length_total_utr/total_utr))
     with open(os.path.join(args.outputPath, args.outputFile), mode="w") as oFile:
         oFile.write("seqname\tstart\tend\tlength\tsequence\tlabel\n")