Parser file added.

pybedtools_parser.py

@@ -0,0 +1,32 @@
+def parsing_bed(bed_file):
+    def check_int(line):
+        try:
+            line[1], line[2] = int(line[1]), int(line[2])
+        except ValueError:
+            raise ValueError("Program expects starting and "
+                             "ending positions to be valid "
+                             "numbers (integer). Check line: {} "
+                             .format(' '.join(line)))
+        return line
+
+    def check_len(line):
+        try:
+            line[2]
+        except IndexError:
+            raise IndexError("Program expects each line to "
+                             "have chromosome name, starting "
+                             "and ending position. Check line: {} "
+                             .format(' '.join(line)))
+        return line
+
+    parsed_data = list()
+    with open(bed_file) as input_handle:
+        for line in input_handle:
+            line_elements = line.split()
+            # Ignore annotation lines.
+            if any(el in line_elements for el in ("#", "browser", "track")):
+                continue
+            check_len(line_elements)
+            check_int(line_elements)
+            parsed_data.append(tuple(line_elements[0:5]))
+        return parsed_data