bit_compression.py

class CompressedGene:
 def __init__(self, gene: str) -> None:
 self._compress(gene)

 def __str__(self) -> str: # string representation for pretty printing
 return self.decompress()

 def _compress(self, gene: str) -> None:
 self.bit_string: int = 1 # start with sentinel
 for nucleotide in gene.upper():
 self.bit_string <<= 2 # shift left two bits
 if nucleotide == 'A': # change last two bits to 00
 self.bit_string |= 0b00
 elif nucleotide == 'C': # change last two bits to 01
 self.bit_string |= 0b01
 elif nucleotide == 'G': # change last two bits to 10
 self.bit_string |= 0b10
 elif nucleotide == 'T': # change last two bits to 11
 self.bit_string |= 0b11
 else:
 raise ValueError('Invalid Nucleotide:{}'.format(nucleotide))

 def decompress(self) -> str:
 gene: str = ''
 for i in range(0, self.bit_string.bit_length() - 1, 2): # - 1 to exclude sentinel
 bits: int = self.bit_string >> i & 0b11 # get just 2 relevant bits
 if bits == 0b00: # A
 gene += 'A'
 elif bits == 0b01: # C
 gene += 'C'
 elif bits == 0b10: # G
 gene += 'G'
 elif bits == 0b11: # T
 gene += 'T'
 else:
 raise ValueError('Invalid bits:{}'.format(bits))
 return gene[::-1] # [::-1] reverses string by slicing backward