Convert seqnames and strand for generic use when exporting as pandas …

…data frame (#82) Also updated tests
BiocPy · Apr 18, 2024 · 0546dbd · 0546dbd
1 parent b3e59e1
commit 0546dbd
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Showing 2 changed files with 15 additions and 2 deletions.
diff --git a/src/genomicranges/GenomicRanges.py b/src/genomicranges/GenomicRanges.py
@@ -1043,8 +1043,8 @@ def to_pandas(self) -> "pandas.DataFrame":
         import pandas as pd
 
         _rdf = self._ranges.to_pandas()
-        _rdf["seqnames"] = self._seqnames
-        _rdf["strand"] = self._strand
+        _rdf["seqnames"] = self.get_seqnames()
+        _rdf["strand"] = self.get_strand(as_type="list")
 
         if self._names is not None:
             _rdf.index = self._names

diff --git a/tests/test_gr_methods_basic.py b/tests/test_gr_methods_basic.py
@@ -89,3 +89,16 @@ def test_export():
 
     assert df is not None
     assert df.shape[0] == len(gr)
+    assert df["seqnames"].tolist() == [
+        "chr1",
+        "chr2",
+        "chr2",
+        "chr2",
+        "chr1",
+        "chr1",
+        "chr3",
+        "chr3",
+        "chr3",
+        "chr3",
+    ]
+    assert df["strand"].tolist() == ["-", "+", "+", "*", "*", "+", "+", "+", "-", "-"]