change requirement in setup.py and comment in BED reading

Author: pavanvidem

hicexplorer/test/general/test_hicCorrectMatrix.py

@@ -17,15 +17,13 @@
 
 
 def are_files_equal(file1, file2, pDifference=1):
-    equal = True
     with open(file1) as textfile1, open(file2) as textfile2:
         for x, y in zip(textfile1, textfile2):
             if x != y:
                 count = sum(1 for a, b in zip(x, y) if a != b)
                 if count > pDifference:
-                    equal = False
-                    break
-    return equal
+                    return False
+    return True
 
 
 def test_correct_matrix_ICE():

hicexplorer/utilities.py

@@ -56,6 +56,7 @@ def readTargetBed(pBedFile):
             try:
                 chrom, start, end = _line[:4]
             except ValueError:
+                # in case the BED is space seprated instead of tabs, split it by whitespaces
                 _line = line.strip().split()
                 chrom, start, end, gene = _line[:4]
             if gene not in present_genes[outer_matrix][inner_matrix]:

setup.py

@@ -116,7 +116,7 @@ def checkProgramIsInstalled(self, program, args, where_to_download,
                        "tqdm >= 4.66",
                        "hyperopt >= 0.2.7",
                        "graphviz >= 0.20",
-                       "scikit-learn == 1.3.2",
+                       "scikit-learn >= 1.3,<1.4",
                        "imbalanced-learn >= 0.11",
                        "cleanlab >= 2.5"
                        ]