Upload sequence.py

sequence.py

@@ -0,0 +1,72 @@
+class Sequence:
+    def __init__(self, sequence):
+        self.sequence = sequence.lower()
+
+    def get_seq_length(self):
+        return len(self.sequence)
+        # Total length of sequence
+
+    def get_unit_count(self, unit):
+        unit = unit.lower()
+        return self.sequence.count(unit)
+        # Unit count of specified unit in sequence
+
+    def get_unit_percentage(self, unit):
+        total_units = self.get_seq_length()
+        unit_count = self.get_unit_count(unit)
+        unit_percentage = (unit_count / total_units) * 100
+        return unit_percentage
+        # unit percentage for specified unit in sequence
+
+    def get_unit_at_position(self, position):
+        pos = position - 1
+
+        if 0 <= pos < len(self.sequence):
+            base_at_pos = self.sequence[pos]
+            return base_at_pos
+        else:
+            return "Position is out of range. Positions should be 1 - {}".format(len(self.sequence))
+        # Returns the unit at a specified position in the sequence
+
+    def get_unit_at_positions(self, position_list):
+        if self.check_positions(position_list):
+            pos_dict = {i: self.sequence[i - 1] for i in position_list if 0 <= i < len(self.sequence)}
+            return pos_dict
+        else:
+            return "Position is out of range.Positions should be 1 - {}".format(len(self.sequence))
+        # Returns unit for each position in list
+
+    def check_positions(self, position_list):
+        # Check if the positions are within the range of the sequence length
+        # Value = 0 -> position out of sequence range
+        # Value = 1 -> position within sequence range
+
+        checked = {}
+        for pos in position_list:
+            if pos <= 0 or pos > len(self.sequence):
+                checked[pos] = 0
+            else:
+                checked[pos] = 1
+
+        # Check if all values are equal to 1 / All positions in the list are within the range of the sequence length
+        all_values_equal_to_1 = all(value == 1 for value in checked.values())
+
+        if all_values_equal_to_1:
+            valid = True
+        else:
+            valid = False
+
+        return valid
+
+    def get_subsequence(self, start_position, end_position):
+        # Ensure the start and end positions are within the bounds of the sequence
+        if start_position > 0 and end_position <= len(self.sequence):
+            return self.sequence[start_position - 1:end_position]
+        else:
+            return "Position is out of range. Positions should be 1 - {}".format(len(self.sequence))
+        # Returns the subsequence based on given positions
+
+    def subsequence_total_units(self, start_position, end_position):
+        return len(self.get_subsequence(start_position, end_position))
+        # Returns the total number of units in the subsequence
+