Script for bed parsing has added

Merge.py

@@ -0,0 +1,33 @@
+def divide(sort_result, list_chr_names):
+    divided_by_chr = []
+    for i in list_chr_names:
+        name = i
+        i = list()
+        for j in range(len(sort_result)):
+            if sort_result[j][0] == name:
+                i.append(sort_result[j])
+        divided_by_chr.append(i)
+    return divided_by_chr
+
+
+def merge_by_chr(temp_tuple):
+    merged = [temp_tuple[0]]
+    for current in temp_tuple:
+        previous = merged[-1]
+        if current[1] <= previous[2]:
+            previous[2] = max(previous[2], current[2])
+        else:
+            merged.append(current)
+    return merged
+
+
+def merge(bed_entries: list):
+    result = list()
+    names = set()
+    for i in bed_entries:
+        names.add(i[0])
+    names = sorted(list(names))
+    divided_by_chr = divide(bed_entries, names)
+    for i in divided_by_chr:
+        result.append(merge_by_chr(i))
+    return result

Parse.py

@@ -0,0 +1,15 @@
+def parse(bed_file):
+
+    def check(our_line):
+        try:
+            our_line[1] = int(our_line[1])
+            our_line[2] = int(our_line[2])
+        except ValueError:
+            raise ValueError("{0} is not an int".format(our_line))
+        return our_line
+
+    result = list()
+    with open(bed_file, 'r') as file:
+        for line in file:
+            result.append(check(line.split()))
+    return result

Sort.py

@@ -0,0 +1,2 @@
+def sort(bed_entries: list):
+    return sorted(bed_entries, key=lambda x: (x[0], x[1]))