update the return values for cage and regulatory elements

genomics-long-range-benchmark.py

@@ -175,9 +175,9 @@ class CagePredictionHandler(GenomicLRATaskHandler):
                 # chromosome number
                 "chromosome": datasets.Value(dtype="string"),
                 # start
-                "start": datasets.Value(dtype="int32"),
+                "labels_start": datasets.Value(dtype="int32"),
                 # stop
-                "stop": datasets.Value(dtype="int32")
+                "labels_stop": datasets.Value(dtype="int32")
             }
         )
         return datasets.DatasetInfo(
@@ -261,11 +261,12 @@ class CagePredictionHandler(GenomicLRATaskHandler):
 
             chromosome = row['chrom']
 
-            padded_sequence = pad_sequence(
+            padded_sequence,new_start,new_stop = pad_sequence(
                 chromosome=self.reference_genome[chromosome],
                 start=start,
                 sequence_length=self.sequence_length,
                 end=stop,
+                return_new_start_stop=True
             )
 
             # floor npy_idx to the nearest 1000
@@ -291,8 +292,8 @@ class CagePredictionHandler(GenomicLRATaskHandler):
                     "labels": targets,
                     "sequence": standardize_sequence(padded_sequence),
                     "chromosome": re.sub("chr", "", chromosome),
-                    "start": int(row["start"]),
-                    "stop": int(row["stop"])
+                    "labels_start": new_start,
+                    "labels_stop": new_stop
                 }
                 key += 1
 
@@ -701,8 +702,10 @@ class ChromatinFeaturesHandler(GenomicLRATaskHandler):
                 "labels": datasets.Sequence(datasets.Value("int8")),
                 # chromosome number
                 "chromosome": datasets.Value(dtype="string"),
-                # position
-                "position": datasets.Value(dtype="int32"),
+                # starting position in genome which corresponds to label
+                "label_start": datasets.Value(dtype="int32"),
+                # end position in genome which corresponds to label
+                "label_stop": datasets.Value(dtype="int32"),
             }
         )
         return datasets.DatasetInfo(
@@ -755,7 +758,8 @@ class ChromatinFeaturesHandler(GenomicLRATaskHandler):
                     "labels": labels_row,
                     "sequence": standardize_sequence(padded_sequence),
                     "chromosome": re.sub("chr", "", chromosome),
-                    "position": coordinates_row['POS']
+                    "label_start": coordinates_row['POS']-100,
+                    "label_stop": coordinates_row['POS'] + 99,
                 }
                 key += 1
 
@@ -808,9 +812,9 @@ class RegulatoryElementHandler(GenomicLRATaskHandler):
                 # chromosome number
                 "chromosome": datasets.Value(dtype="string"),
                 # start
-                "start": datasets.Value(dtype="int32"),
+                "label_start": datasets.Value(dtype="int32"),
                 # stop
-                "stop": datasets.Value(dtype="int32"),
+                "label_stop": datasets.Value(dtype="int32"),
             }
         )
         return datasets.DatasetInfo(
@@ -866,8 +870,8 @@ class RegulatoryElementHandler(GenomicLRATaskHandler):
                     "labels": label,
                     "sequence": standardize_sequence(padded_sequence),
                     "chromosome": re.sub("chr", "", chromosome),
-                    "start": coordinates_row["START"],
-                    "stop": coordinates_row["STOP"]
+                    "label_start": coordinates_row["START"],
+                    "label_stop": coordinates_row["STOP"]
                 }
                 key += 1
 
@@ -962,7 +966,8 @@ def standardize_sequence(sequence: str):
     return sequence
 
 
-def pad_sequence(chromosome, start, sequence_length, end=None, negative_strand=False):
+def pad_sequence(chromosome, start, sequence_length, end=None, negative_strand=False,
+                 return_new_start_stop=False):
     """
     Extends a given sequence to length sequence_length. If
     padding to the given length is outside the gene, returns
@@ -989,5 +994,12 @@ def pad_sequence(chromosome, start, sequence_length, end=None, negative_strand=F
     if start < 0 or end >= len(chromosome):
         return
     if negative_strand:
+        if return_new_start_stop:
+            return chromosome[start:end].reverse.complement.seq ,start, end
+
         return chromosome[start:end].reverse.complement.seq
+
+    if return_new_start_stop:
+        return chromosome[start:end].seq , start, end
+
     return chromosome[start:end].seq