Maximum neighbourhood approach

Scripts/SyntenyLink_mn.py

+## Some sorting functions
+
+### 1. To compare the whether two subgenomes are two different strands of the same genes
+
+    #If true: Output is 1
+    #If false: Output is 2
+
+def compare_strands_subgenomes(string1, string2):
+    # a function to test if two given subgenomes are forward or reverse strands
+    if len(string1) == len(string2)+2 or len(string2)==len(string1)+2:
+        count=0
+        m=max(len(string1),len(string2))
+        for i in range(m-2):
+            # Compare characters at the same position
+            if string1[i] == string2[i]:
+                count=count+1
+        if count==m-2:
+            return 1
+        else:
+            return 0
+    else:
+        #they are not forward and reverse strand
+        return 0
+    # Iterate through three character in both strings
+
+def compare_subgenomes(string1, string2):
+  if string1==string2 or compare_strands_subgenomes(string1, string2):
+     return 1
+  else:
+     return 0
+
+### Function for Counting occureneces of a given chromosome in a given array
+def count_occurrences(array, entry):
+    if len(array) == 0:
+        print("\n Empty array")
+    count = 0
+    for elem in array:
+        if elem == entry:
+            count += 1
+    return count
+# Example usage:
+given_array = ["N1", "N2", "N3.r", "N4", "N2", "N5", "N2"]
+given_entry = "N3.r"
+
+occurrences = count_occurrences(given_array, given_entry)
+# print("Number of occurrences:", occurrences)
+    
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