Fix for by_distance

coolpuppy/coolpup.py

@@ -575,7 +575,6 @@ def get_combinations(
         groupby=[],
         modify_2Dintervals_func=None,
     ):
-
         if intervals is None:
             intervals = self.intervals
         if not len(intervals) >= 1:
@@ -734,7 +733,6 @@ def get_intervals_stream(
         groupby=[],
         modify_2Dintervals_func=None,
     ):
-
         if intervals is None:
             intervals = self.intervals
         intervals = filter_func1(intervals)
@@ -927,8 +925,10 @@ def __init__(
                 except Exception as e:
                     raise ValueError("provided expected is not valid") from e
                 self.ExpSnipper = snipping.ExpectedSnipper(
-                    self.clr, self.expected, view_df=self.view_df,
-                    expected_value_col=self.expected_value_col
+                    self.clr,
+                    self.expected,
+                    view_df=self.view_df,
+                    expected_value_col=self.expected_value_col,
                 )
                 self.expected_selections = {
                     region_name: self.ExpSnipper.select(region_name, region_name)
@@ -2006,12 +2006,17 @@ def pileup(
     pileup_df - pandas DataFrame containing the pileups and their grouping information,
     if any, all possible annotations from the arguments of this function.
     """
-    if by_distance:
+    if by_distance is not False:
         if by_distance is True or by_distance == "default":
             distance_edges = "default"
             by_distance = True
         elif len(by_distance) > 0:
-            distance_edges = by_distance
+            try:
+                distance_edges = [int(i) for i in by_distance]
+            except Exception as e:
+                raise ValueError(
+                    "Distance bin edges have to be an iterable of integers or convertable to integers"
+                ) from e
             by_distance = True
         else:
             raise ValueError(
@@ -2021,8 +2026,6 @@ def pileup(
             raise ValueError(
                 "Can't do local pileups by distance, please specify only one of those arguments"
             )
-    else:
-        by_distance = False
 
     if not rescale:
         rescale_flank = None

tests/test_coolpup.py

@@ -7,7 +7,7 @@
 """
 
 from matplotlib.pyplot import ioff
-from coolpuppy.coolpup import PileUpper, CoordCreator
+from coolpuppy.coolpup import PileUpper, CoordCreator, pileup
 from cooltools.lib import io, common
 import pandas as pd
 import numpy as np
@@ -101,16 +101,34 @@ def test_bystrand_bydistance_pileups_with_controls(request):
     features = bf.read_table(
         op.join(request.fspath.dirname, "data/toy_features.bed"), schema="bed"
     )
-    cc = CoordCreator(
-        features,
-        1_000_000,
+
+    pup = pileup(
+        clr=clr,
+        features=features,
         features_format="bed",
-        local=False,
+        view_df=regions,
+        mindist=0,
         flank=2_000_000,
+        nshifts=1,
+        by_strand=True,
+        by_distance=True,
+    )
+    assert np.all(
+        pup.sort_values(["orientation", "distance_band"])["n"] == [1, 2, 1, 1, 1, 6]
+    )
+
+    distance_bins = np.append([0], 50000 * 2 ** np.arange(30))
+    pup = pileup(
+        clr=clr,
+        features=features,
+        features_format="bed",
+        view_df=regions,
         mindist=0,
+        flank=2_000_000,
+        nshifts=1,
+        by_strand=True,
+        by_distance=distance_bins,
     )
-    pu = PileUpper(clr, cc, expected=False, view_df=regions, control=True)
-    pup = pu.pileupsByStrandByDistanceWithControl()
     assert np.all(
         pup.sort_values(["orientation", "distance_band"])["n"] == [1, 2, 1, 1, 1, 6]
     )