Treat Series input like dict for chromsizes and midpoints

Author: nvictus

bioframe/extras.py

@@ -28,15 +28,15 @@ def make_chromarms(
 
     Parameters
     ----------
-    chromsizes : pandas.Dataframe or pandas.Series
-        If pandas.Series, a map from chromosomes to lengths in bp.
+    chromsizes : pandas.Dataframe or dict-like
+        If dict or pandas.Series, a map from chromosomes to lengths in bp.
         If pandas.Dataframe, a dataframe with columns defined by cols_chroms.
         If cols_chroms is a triplet (e.g. 'chrom','start','end'), then
         values in chromsizes[cols_chroms[1]].values must all be zero.
 
     midpoints : pandas.Dataframe or dict-like
         Mapping of chromosomes to midpoint (aka centromere) locations.
-        If pandas.Series, a map from chromosomes to midpoints in bp.
+        If dict or pandas.Series, a map from chromosomes to midpoints in bp.
         If pandas.Dataframe, a dataframe with columns defined by cols_mids.
 
     cols_chroms : (str, str) or (str, str, str)
@@ -59,9 +59,13 @@ def make_chromarms(
     elif len(cols_chroms) == 3:
         ck1, sk1, ek1 = cols_chroms
 
-    if isinstance(chromsizes, pd.Series):
+    if isinstance(chromsizes, (pd.Series, dict)):
+        chromsizes = dict(chromsizes)
         df_chroms = (
-            pd.DataFrame(chromsizes).reset_index().rename(columns={"index": ck1})
+            pd.DataFrame({
+                ck1: list(chromsizes.keys()),
+                "length": list(chromsizes.values()),
+            })
         )
     elif isinstance(chromsizes, pd.DataFrame):
         df_chroms = chromsizes.copy()
@@ -83,7 +87,8 @@ def make_chromarms(
         raise ValueError("invalid number of cols_chroms")
 
     ck2, sk2 = cols_mids
-    if isinstance(midpoints, dict):
+    if isinstance(midpoints, (pd.Series, dict)):
+        midpoints = dict(midpoints)
         df_mids = pd.DataFrame.from_dict(midpoints, orient="index", columns=[sk2])
         df_mids.reset_index(inplace=True)
         df_mids.rename(columns={"index": ck2}, inplace=True)

tests/test_extras.py

@@ -12,46 +12,59 @@
 def test_make_chromarms():
 
     ### test the case where columns have different names
-    df1 = pd.DataFrame(
+    df = pd.DataFrame(
         [["chrX", 0, 8]],
         columns=["chromosome", "lo", "hi"],
     )
-
-    df2 = pd.DataFrame([["chrX", 4]], columns=["chromosome", "loc"])
-
-    df_result = pd.DataFrame(
+    mids = pd.DataFrame([["chrX", 4]], columns=["chromosome", "loc"])
+    arms = pd.DataFrame(
         [
             ["chrX", 0, 4, "chrX_p"],
             ["chrX", 4, 8, "chrX_q"],
         ],
-        columns=["chromosome", "lo", "hi", "name"],
+        columns=["chrom", "start", "end", "name"],
     )
+    arms = arms.astype({"start": pd.Int64Dtype(), "end": pd.Int64Dtype()})
 
     # test passing 3 columns
+    result = bioframe.make_chromarms(
+        df,
+        mids,
+        cols_chroms=["chromosome", "lo", "hi"],
+        cols_mids=["chromosome", "loc"],
+    )
     pd.testing.assert_frame_equal(
-        df_result.astype({"lo": pd.Int64Dtype(), "hi": pd.Int64Dtype()}),
-        bioframe.make_chromarms(
-            df1,
-            df2,
-            cols_chroms=["chromosome", "lo", "hi"],
-            cols_mids=["chromosome", "loc"],
-        ),
+        result,
+        arms.rename(columns={"chrom": "chromosome", "start": "lo", "end": "hi"})
     )
 
     # test passing 2 columns
+    result = bioframe.make_chromarms(
+        df,
+        mids,
+        cols_chroms=["chromosome", "hi"],
+        cols_mids=["chromosome", "loc"],
+    )
     pd.testing.assert_frame_equal(
-        df_result.astype({"lo": pd.Int64Dtype(), "hi": pd.Int64Dtype()}).rename(
-            columns={"lo": "start", "hi": "end"}
-        ),
-        bioframe.make_chromarms(
-            df1,
-            df2,
-            cols_chroms=["chromosome", "hi"],
-            cols_mids=["chromosome", "loc"],
-        ),
+        result
+        arms.rename(columns={"chrom": "chromosome"}),
     )
 
-    # todo: test for passing pd.series !
+    # test for passing Series or dict
+    result = bioframe.make_chromarms(pd.Series({"chrX": 8}), mids, cols_mids=["chromosome", "loc"])
+    pd.testing.assert_frame_equal(arms, result)
+
+    result = bioframe.make_chromarms(pd.Series({"chrX": 8}), pd.Series({"chrX": 4}))
+    pd.testing.assert_frame_equal(arms, result)
+
+    bioframe.make_chromarms({"chrX": 8}, mids, cols_mids=["chromosome", "loc"])
+    pd.testing.assert_frame_equal(arms, result)
+
+    bioframe.make_chromarms({"chrX": 8}, pd.Series({"chrX": 4}))
+    pd.testing.assert_frame_equal(arms, result)
+
+    bioframe.make_chromarms({"chrX": 8}, {"chrX": 4})
+    pd.testing.assert_frame_equal(arms, result)
 
 
 def test_binnify():