Fix the to_pandas method when names are available

CHANGELOG.md

@@ -1,12 +1,13 @@
 # Changelog
 
-## Version 0.8.0 - 0.8.4
+## Version 0.8.0 - 0.8.5
 
 - Rename `GenomicRangesList` to `CompressedGenomicRangesList` and now extends compressed-lists.
 - Classes extend `BiocObject` from biocutils, provides a default metadata attribute and helper functions.
 - Rename `validate` to `_validate` for consistency with the rest of the packages and classes.
 - Fix for empty compressed genomic ranges list.
 - Aliases `GRanges` and `CompressedGRangesList`.
+- Fixed a bug in `to_pandas()` when `names` and `mcols` are present.
 
 ## Version 0.7.0 - 0.7.3
 

src/genomicranges/GenomicRanges.py

@@ -1006,13 +1006,13 @@ def to_pandas(self):
         _rdf["seqnames"] = self.get_seqnames()
         _rdf["strand"] = self.get_strand(as_type="list")
 
-        if self._names is not None:
-            _rdf.index = self._names
-
         if self._mcols is not None:
             if self._mcols.shape[1] > 0:
                 _rdf = pd.concat([_rdf, self._mcols.to_pandas()], axis=1)
 
+        if self._names is not None:
+            _rdf.index = list(self._names)
+
         return _rdf
 
     @classmethod
@@ -1085,10 +1085,12 @@ def to_polars(self):
         import polars as pl
 
         _rdf = self._ranges.to_polars()
-        _rdf = _rdf.with_columns(seqnames=self.get_seqnames(), strand=self.get_strand(as_type="list"))
+        _rdf = _rdf.with_columns(
+            seqnames=pl.Series(self.get_seqnames()), strand=pl.Series(self.get_strand(as_type="list"))
+        )
 
         if self._names is not None:
-            _rdf = _rdf.with_columns(rownames=self._names)
+            _rdf = _rdf.with_columns(rownames=pl.Series(list(self._names)))
 
         if self._mcols is not None:
             if self._mcols.shape[1] > 0:

tests/test_gr_basic.py

@@ -113,6 +113,44 @@ def test_export_pandas_with_mcols():
     assert isinstance(df, pd.DataFrame)
 
 
+def test_export_pandas_with_names_and_mcols():
+    from biocframe import BiocFrame
+    from iranges import IRanges
+
+    ranges = IRanges(start=[0, 10, 20], width=[5, 5, 5])
+    mcols = BiocFrame({"gene_id": ["g1", "g2", "g3"], "gene_name": ["A", "B", "C"]})
+    gr_named = GenomicRanges(
+        seqnames=["1", "1", "1"],
+        ranges=ranges,
+        strand=["+", "+", "-"],
+        names=["g1", "g2", "g3"],
+        mcols=mcols,
+    )
+    df = gr_named.to_pandas()
+    assert df is not None
+    assert df.shape == (3, 7)
+    assert df.index.tolist() == ["g1", "g2", "g3"]
+
+
+def test_export_polars_with_names_and_mcols():
+    from biocframe import BiocFrame
+    from iranges import IRanges
+
+    ranges = IRanges(start=[0, 10, 20], width=[5, 5, 5])
+    mcols = BiocFrame({"gene_id": ["g1", "g2", "g3"], "gene_name": ["A", "B", "C"]})
+    gr_named = GenomicRanges(
+        seqnames=["1", "1", "1"],
+        ranges=ranges,
+        strand=["+", "+", "-"],
+        names=["g1", "g2", "g3"],
+        mcols=mcols,
+    )
+    df = gr_named.to_polars()
+    assert df is not None
+    assert df.shape == (3, 8)  # 8 because polars adds a 'rownames' column
+    assert df["rownames"].to_list() == ["g1", "g2", "g3"]
+
+
 def test_combine():
     g_src = GenomicRanges(
         seqnames=["chr1", "chr2", "chr1", "chr3", "chr2"],