Merge branch 'main' of https://huggingface.co/datasets/InstaDeepAI/multi_omics_transcript_expression

multi_omics_transcript_expression.py

@@ -226,6 +226,7 @@ class TranscriptExpressionHandler(GenomicLRATaskHandler):
         self,
         sequence_length: int = DEFAULT_LENGTH,
         filter_out_sequence_length: int = DEFAULT_FILTER_OUT_LENGTH,
+        expression_method: str = "read_counts_old",
         **kwargs,
     ):
         """
@@ -237,12 +238,15 @@ class TranscriptExpressionHandler(GenomicLRATaskHandler):
             coordinate_csv_file: The csv file that stores the coordinates and filename of the target
             labels_csv_file: The csv file that stores the labels with one sample per row.
             sequence_length: Sequence length for this handler.
+            expression_method: To specify if user wants to use TPMs instead of read
+                counts.
         """
         self.reference_genome = None
         self.coordinate_csv_file = None
         self.labels_csv_file = None
         self.sequence_length = sequence_length
         self.filter_out_sequence_length = filter_out_sequence_length
+        self.expression_method = expression_method
 
         if filter_out_sequence_length is not None:
             assert isinstance(filter_out_sequence_length, int)
@@ -293,9 +297,18 @@ 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_tpm_multiomics.csv"
-        )
+        if self.expression_method == "tpm":
+            self.df_csv_file = dl_manager.download_and_extract(
+                "transcript_expression/GTEx_final_tpm_multiomics.csv"
+            )
+        elif self.expression_method == "read_counts_old":
+            self.df_csv_file = dl_manager.download_and_extract(
+                "transcript_expression/GTEx_v1_multiomics.csv"
+            )
+        elif self.expression_method == "read_counts":
+            raise NotImplementedError(
+                "Needs the dataset"
+            )
 
         return super().split_generators(dl_manager, cache_dir_root)
 
@@ -338,9 +351,9 @@ class TranscriptExpressionHandler(GenomicLRATaskHandler):
                     "DNA": standardize_sequence(padded_sequence),
                     "chromosome": re.sub("chr", "", chromosome),
                     "RNA": coordinates_row["RNA"],
-                    # "five_prime_utr": coordinates_row["5UTR"],
-                    # "coding_sequence": coordinates_row["CDS"],
-                    # "three_prime_utr": coordinates_row["3UTR"],
+                    "five_prime_utr": coordinates_row["5UTR"],
+                    "coding_sequence": coordinates_row["CDS"],
+                    "three_prime_utr": coordinates_row["3UTR"],
                     "Protein": coordinates_row["Protein"],
                 }
                 key += 1

transcript_expression/GTEx_tpm_multiomics.csv

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:c26aac2b9f4f1ab97f800337a36294c3cc99eb18c16ad7e99967183b43810908
-size 446177061

transcript_expression/expression_values_v1.csv

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:33497cd1e5ace0eee4f220319dd16bfa5b9b0befae9c6fa95b8abc3d62f5e1fc
-size 457970509

transcript_expression/expression_values_v2.csv

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:a188b731d7e9ec28ac8dd723d4d0bee597bbd4f8b4ba78707875e7a868ed778a
-size 539601860