add UTR info

multi_omics_transcript_expression.py

@@ -266,6 +266,9 @@ class TranscriptExpressionHandler(GenomicLRATaskHandler):
                 # chromosome number
                 "chromosome": datasets.Value(dtype="string"),
                 "RNA": datasets.Value("string"),
+                "five_prime_utr": datasets.Value("five_prime_utr"),
+                "coding_sequence": datasets.Value("coding_sequence"),
+                "three_prime_utr": datasets.Value("three_prime_utr"),
                 "Protein": datasets.Value("string"),
                 "transcript_id": datasets.Value("string"),
                 "gene_id": datasets.Value("string"),
@@ -291,7 +294,7 @@ class TranscriptExpressionHandler(GenomicLRATaskHandler):
         self.reference_genome = Fasta(reference_genome_file, one_based_attributes=False)
 
         self.df_csv_file = dl_manager.download_and_extract(
-            "transcript_expression/GTEx_df_v1.csv"
+            "transcript_expression/GTEx_df_v1_with_utr.csv"
         )
 
         return super().split_generators(dl_manager, cache_dir_root)
@@ -330,6 +333,9 @@ class TranscriptExpressionHandler(GenomicLRATaskHandler):
                     "DNA": standardize_sequence(padded_sequence),
                     "chromosome": re.sub("chr", "", chromosome),
                     "RNA": coordinates_row["RNA"],
+                    "five_prime_utr": coordinates_row["five_prime_utr"],
+                    "coding_sequence": coordinates_row["coding_sequence"],
+                    "three_prime_utr": coordinates_row["three_prime_utr"],
                     "Protein": coordinates_row["Protein"],
                 }
                 key += 1