add new dataset with correct UTRs

.gitattributes

@@ -57,3 +57,4 @@ 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
 transcript_expression/GTEx_df_v2_with_utr.csv filter=lfs diff=lfs merge=lfs -text
 transcript_expression/GTEx_df_v1_with_utr.csv filter=lfs diff=lfs merge=lfs -text
+transcript_expression/GTEx_v1_multiomics.csv filter=lfs diff=lfs merge=lfs -text

multi_omics_transcript_expression.py

@@ -294,7 +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_with_utr.csv"
+            "transcript_expression/GTEx_v1_multiomics.csv"
         )
 
         return super().split_generators(dl_manager, cache_dir_root)
@@ -313,7 +313,12 @@ class TranscriptExpressionHandler(GenomicLRATaskHandler):
 
         key = 0
         for idx, coordinates_row in split_df.iterrows():
-            start = coordinates_row["position"] - 1  # -1 since vcf coords are 1-based
+            negative_strand = coordinates_row["strand"] == "-"
+
+            if negative_strand:
+                start =  coordinates_row["end"] - 1
+            else:
+                start = coordinates_row["start"] - 1  # -1 since vcf coords are 1-based
 
             chromosome = coordinates_row["chr"]
             labels_row = coordinates_row[LABELS_V1]
@@ -321,7 +326,7 @@ class TranscriptExpressionHandler(GenomicLRATaskHandler):
                 chromosome=self.reference_genome[chromosome],
                 start=start,
                 sequence_length=self.sequence_length,
-                negative_strand=coordinates_row["strand"] == "-",
+                negative_strand=negative_strand,
                 filter_out_sequence_length=self.filter_out_sequence_length,
             )
             if padded_sequence:

transcript_expression/GTEx_v1_multiomics.csv

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:7ea6fde2f3f6278fe956bba63e100947ead8fce5ea3c6d3718aaf7b1f99a782e
+size 643913393