1 #! /usr/bin/python
  2
  3 # Linux And Python Programming
  4 # Hand-in 5
  5 # 5. October 2007
  6
  7 class Seq:
  8   """
  9   Class defining generel methods for a biological sequence
 10   """
 11
 12   def __init__(self, seq, pattern):
 13     """
 14     Constructor method. Checks whether an input-sequence is a legal biological
 15     sequence
 16
 17     seq -- the input sequence
 18     pattern -- the pattern that determines if the sequence is invalid
 19     """
 20
 21     if pattern.search(seq):
 22       print " Warning: sequence contains illegal characters"
 23     self.data = seq.upper()
 24
 25   def __getitem__(self, index):
 26     """
 27     Return element
 28
 29     index -- the position of the element wished to be returned
 30     """
 31     return self.data[index]
 32
 33   def __len__(self):
 34     """
 35     Returns the length of the sequence
 36     """
 37     return len(self.data)
 38
 39
 40 class Dna(Seq):
 41   """
 42   Class defining methods for a DNA sequence
 43   """
 44
 45   def __init__(self, seq):
 46     """
 47     Constructor method.
 48
 49     seq -- the input sequence
 50     """
 51     import re
 52
 53     patternString = '[AGCTagct]+'
 54
 55     pattern = re.compile(patternString)
 56
 57     Seq.__init__(self,seq,pattern)
 58
 59   def __repr__ ( self ):
 60     """
 61     Return data attribute
 62     """
 63
 64     return self .data
 65
 66
 67
 68 if __name__ == "__main__":
 69   d = Dna('ACCCGT')