fix

.gitattributes

@@ -53,6 +53,5 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 *.jpg filter=lfs diff=lfs merge=lfs -text
 *.jpeg filter=lfs diff=lfs merge=lfs -text
 *.webp filter=lfs diff=lfs merge=lfs -text
-transcript_expression/expression_values_v1.csv filter=lfs diff=lfs merge=lfs -text
-transcript_expression/expression_values_v2.csv filter=lfs diff=lfs merge=lfs -text
-transcript_expression/transcript_coordinates.csv filter=lfs diff=lfs merge=lfs -text
+transcript_expression/GTEx_df_v1.csv filter=lfs diff=lfs merge=lfs -text
+transcript_expression/GTEx_df_v2.csv filter=lfs diff=lfs merge=lfs -text

multi_omics_transcript_expression.py

@@ -32,6 +32,96 @@ Task Specific Handlers:
 logger = logging.getLogger("multi_omics_transcript_expression")
 logger.setLevel("INFO")
 
+LABELS_V1 = [
+    "Adipose Tissue",
+    "Adrenal Gland",
+    "Bladder",
+    "Blood",
+    "Blood Vessel",
+    "Brain",
+    "Breast",
+    "Cervix Uteri",
+    "Colon",
+    "Esophagus",
+    "Fallopian Tube",
+    "Heart",
+    "Kidney",
+    "Liver",
+    "Lung",
+    "Muscle",
+    "Nerve",
+    "Ovary",
+    "Pancreas",
+    "Pituitary",
+    "Prostate",
+    "Salivary Gland",
+    "Skin",
+    "Small Intestine",
+    "Spleen",
+    "Stomach",
+    "Testis",
+    "Thyroid",
+    "Uterus",
+    "Vagina",
+]
+
+LABELS_V2 = [
+    "Adipose_Subcutaneous",
+    "Adipose_Visceral (Omentum)",
+    "Adrenal Gland",
+    "Artery_Aorta",
+    "Artery_Coronary",
+    "Artery_Tibial",
+    "Bladder",
+    "Brain_Amygdala",
+    "Brain_Anterior cingulate cortex (BA24)",
+    "Brain_Caudate (basal ganglia)",
+    "Brain_Cerebellar Hemisphere",
+    "Brain_Cerebellum",
+    "Brain_Cortex",
+    "Brain_Frontal Cortex (BA9)",
+    "Brain_Hippocampus",
+    "Brain_Hypothalamus",
+    "Brain_Nucleus accumbens (basal ganglia)",
+    "Brain_Putamen (basal ganglia)",
+    "Brain_Spinal cord (cervical c-1)",
+    "Brain_Substantia nigra",
+    "Breast_Mammary Tissue",
+    "Cells_Cultured fibroblasts",
+    "Cells_EBV-transformed lymphocytes",
+    "Cervix_Ectocervix",
+    "Cervix_Endocervix",
+    "Colon_Sigmoid",
+    "Colon_Transverse",
+    "Esophagus_Gastroesophageal Junction",
+    "Esophagus_Mucosa",
+    "Esophagus_Muscularis",
+    "Fallopian Tube",
+    "Heart_Atrial Appendage",
+    "Heart_Left Ventricle",
+    "Kidney_Cortex",
+    "Kidney_Medulla",
+    "Liver",
+    "Lung",
+    "Minor Salivary Gland",
+    "Muscle_Skeletal",
+    "Nerve_Tibial",
+    "Ovary",
+    "Pancreas",
+    "Pituitary",
+    "Prostate",
+    "Skin_Not Sun Exposed (Suprapubic)",
+    "Skin_Sun Exposed (Lower leg)",
+    "Small Intestine_Terminal Ileum",
+    "Spleen",
+    "Stomach",
+    "Testis",
+    "Thyroid",
+    "Uterus",
+    "Vagina",
+    "Whole Blood",
+]
+
 
 class GenomicLRATaskHandler(ABC):
     """
@@ -195,12 +285,8 @@ class TranscriptExpressionHandler(GenomicLRATaskHandler):
         )
         self.reference_genome = Fasta(reference_genome_file, one_based_attributes=False)
 
-        self.coordinate_csv_file = dl_manager.download_and_extract(
-            "transcript_expression/transcript_coordinates.csv"
-        )
-
-        self.labels_csv_file = dl_manager.download_and_extract(
-            "transcript_expression/expression_values_v2.csv"
+        self.df_csv_file = dl_manager.download_and_extract(
+            "transcript_expression/GTEx_df_v1.csv"
         )
 
         return super().split_generators(dl_manager, cache_dir_root)
@@ -211,18 +297,17 @@ class TranscriptExpressionHandler(GenomicLRATaskHandler):
         and the corresponding labels. The sequences are padded to the correct sequence
         length and standardized before returning.
         """
-        coordinates_df = pd.read_csv(self.coordinate_csv_file)
-        labels_df = pd.read_csv(self.labels_csv_file)
-        labels_name = labels_df.columns[2:]
+        df = pd.read_csv(self.df_csv_file)
+        labels_name = LABELS_V1
 
-        coordinates_split_df = coordinates_df.loc[coordinates_df["split"] == split]
+        split_df = df.loc[df["split"] == split]
 
         key = 0
-        for idx, coordinates_row in coordinates_split_df.iterrows():
+        for idx, coordinates_row in split_df.iterrows():
             start = coordinates_row["position"] - 1  # -1 since vcf coords are 1-based
 
             chromosome = coordinates_row["chr"]
-            labels_row = labels_df.iloc[idx].values[2:]
+            labels_row = coordinates_row.iloc[LABELS_V1]
             padded_sequence = pad_sequence(
                 chromosome=self.reference_genome[chromosome],
                 start=start,
@@ -241,7 +326,7 @@ class TranscriptExpressionHandler(GenomicLRATaskHandler):
                 }
                 key += 1
         logger.info(
-            f"filtering out {len(coordinates_split_df)-key} "
+            f"filtering out {len(split_df)-key} "
             f"elements from the dataset"
         )
 

transcript_expression/transcript_coordinates.csv

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:6a5ee8afeb870a22e4bc6cef3de694c4107571972f10efe52788122bb87b6820
-size 5237763