fix

multi_omics_transcript_expression.py

@@ -154,7 +154,8 @@ class GenomicLRATaskHandler(ABC):
                 name=datasets.Split.TEST, gen_kwargs={"handler": self, "split": "test"}
             ),
             datasets.SplitGenerator(
-                name=datasets.Split.VALIDATION, gen_kwargs={"handler": self, "split": "test"}
+                name=datasets.Split.VALIDATION,
+                gen_kwargs={"handler": self, "split": "test"},
             ),
         ]
 
@@ -219,8 +220,8 @@ class TranscriptExpressionHandler(GenomicLRATaskHandler):
     Handler for the Transcript Expression task.
     """
 
-    DEFAULT_LENGTH = 200000
-    DEFAULT_FILTER_OUT_LENGTH = 196608
+    DEFAULT_LENGTH = 200_000
+    DEFAULT_FILTER_OUT_LENGTH = 196_608
 
     def __init__(
         self,
@@ -238,7 +239,6 @@ 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
@@ -246,7 +246,6 @@ class TranscriptExpressionHandler(GenomicLRATaskHandler):
         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)
@@ -266,6 +265,10 @@ class TranscriptExpressionHandler(GenomicLRATaskHandler):
                 "DNA": datasets.Value("string"),
                 # list of expression values in each tissue
                 "labels": datasets.Sequence(datasets.Value("float32")),
+                "m_t": datasets.Sequence(datasets.Value("float32")),
+                "sigma_t": datasets.Sequence(datasets.Value("float32")),
+                "m_g": datasets.Sequence(datasets.Value("float32")),
+                "sigma_g": datasets.Sequence(datasets.Value("float32")),
                 "labels_name": datasets.Sequence(datasets.Value("string")),
                 # chromosome number
                 "chromosome": datasets.Value(dtype="string"),
@@ -297,18 +300,12 @@ class TranscriptExpressionHandler(GenomicLRATaskHandler):
         )
         self.reference_genome = Fasta(reference_genome_file, one_based_attributes=False)
 
-        if self.expression_method == "tpm":
-            self.df_csv_file = dl_manager.download_and_extract(
-                "transcript_expression/GTEx_final_tpm_multiomics_fix.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":
-            self.df_csv_file = dl_manager.download_and_extract(
-                "transcript_expression/GTEx_read_counts_multiomics.csv"
-            )
+        self.df_csv_file = dl_manager.download_and_extract(
+            "transcript_expression/GTEx_final_tpm_multiomics_fix.csv"
+        )
+        self.normalization_values_csv_file = dl_manager.download_and_extract(
+            "transcript_expression/normalization_values.csv"
+        )
 
         return super().split_generators(dl_manager, cache_dir_root)
 
@@ -324,12 +321,18 @@ class TranscriptExpressionHandler(GenomicLRATaskHandler):
 
         split_df = df.loc[df["split"] == split]
 
+        norm_values_df = pd.read_csv(self.normalization_values_csv_file)
+        m_t = norm_values_df["m_t"]
+        sigma_t = norm_values_df["sigma_t"]
+        m_g = norm_values_df["m_g"]
+        sigma_g = norm_values_df["sigma_g"]
+
         key = 0
         for idx, coordinates_row in split_df.iterrows():
             negative_strand = coordinates_row["strand"] == "-"
 
             if negative_strand:
-                start =  coordinates_row["end"] - 1
+                start = coordinates_row["end"] - 1
             else:
                 start = coordinates_row["start"] - 1  # -1 since vcf coords are 1-based
 
@@ -342,12 +345,17 @@ class TranscriptExpressionHandler(GenomicLRATaskHandler):
                 negative_strand=negative_strand,
                 filter_out_sequence_length=self.filter_out_sequence_length,
             )
+            fdsjog
             if padded_sequence:
                 yield key, {
-                    "transcript_id":coordinates_row["transcript_id_gtex"],
-                    "gene_id":coordinates_row["gene_id_gtex"],
+                    "transcript_id": coordinates_row["transcript_id_gtex"],
+                    "gene_id": coordinates_row["gene_id_gtex"],
                     "labels_name": labels_name,
                     "labels": labels_row.to_numpy(),
+                    "m_t": m_t.to_numpy(),
+                    "sigma_t": sigma_t.to_numpy(),
+                    "m_g": m_g.to_numpy(),
+                    "sigma_g": sigma_g.to_numpy(),
                     "DNA": standardize_sequence(padded_sequence),
                     "chromosome": re.sub("chr", "", chromosome),
                     "RNA": coordinates_row["RNA"],