fix to get accurate pileups with pysam (deepchem#4121)

sudo-rsingh · Sep 11, 2024 · 632c427 · 632c427
1 parent 5cd9e6f
commit 632c427
Show file tree

Hide file tree

Showing 2 changed files with 7 additions and 8 deletions.
diff --git a/deepchem/data/tests/test_deepvariant_featurizer.py b/deepchem/data/tests/test_deepvariant_featurizer.py
@@ -20,10 +20,12 @@ def test_candidate_windows(self):
         candidate_windows = self.featurizer._featurize(datapoint)
 
         # Assert the number of reads
-        self.assertEqual(len(candidate_windows), 14)
-        self.assertEqual(candidate_windows[13],
-                         ('chr2', 193, 197, 18, 21,
-                          ['GTAAATTGATTTGAATTTTATTTCTTGGTAATGAGG']))
+        self.assertEqual(len(candidate_windows), 15)
+        self.assertEqual(candidate_windows[13][0], 'chr2')
+        self.assertEqual(candidate_windows[13][1], 136)
+        self.assertEqual(candidate_windows[13][2], 137)
+        self.assertEqual(candidate_windows[13][3], 102)
+        self.assertEqual(candidate_windows[13][4], 21)
 
 
 if __name__ == "__main__":

diff --git a/deepchem/feat/bio_seq_featurizer.py b/deepchem/feat/bio_seq_featurizer.py
@@ -200,10 +200,7 @@ def _featurize(self, datapoint):
 
             if (self.get_pileup):
                 pileup_columns = []
-                for pileupcolumn in datapoint.pileup(
-                        reference=record.reference_name,
-                        start=record.reference_start,
-                        end=record.reference_end):
+                for pileupcolumn in datapoint.pileup():
                     pileup_info = {
                         "name":
                             pileupcolumn.reference_name,