Pastebin

  1 class Seq:
  2     """General sequence class"""
  3
  4     def __init__(self, seq, pattern):
  5         """Constructor for Seq.
  6         Takes arguments: seq and pattern"""
  7
  8         if pattern.search(seq):
  9             print "Warning: sequence contains illegal characters"
 10         self.data = seq.upper()
 11
 12     def __getitem__(self, index):
 13         """Returns an item given a specific index"""
 14         return self.data[index]
 15
 16     def __len__(self):
 17         """Returns the size of the data"""
 18         return len(self.data)
 19
 20     def __repr__(self):
 21         """Returns representation of the sequence."""
 22         return self.data
 23
 24
 25 class Dna(Seq):
 26     """DNA sequence class"""
 27     import re
 28     # Valid chars: ACGT
 29     pattern = re.compile("[^ACGTacgt]")
 30
 31     def __init__(self, seq):
 32         self.parent = Seq.__init__(self, seq, self.pattern)
 33
 34     def __repr__(self):
 35         return "DNA sequence: ", repr(self.parent)
 36