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# sequence.py: module of basic sequence methods
# Authors: Brett Bowman, David Alexander
from __future__ import absolute_import
__all__ = [ "complement",
"reverseComplement"]
from string import maketrans
import re
DNA_COMPLEMENT = maketrans('agcturyswkmbdhvnAGCTURYSWKMBDHV-N',
'tcgannnnnnnnnnnnTCGANNNNNNNNNNN-N')
def reverse( sequence ):
"""Return the reverse of any sequence
"""
return sequence[::-1]
def complement( sequence ):
"""
Return the complement of a sequence
"""
if re.search('[^agcturyswkmbdhvnAGCTURYSWKMBDHVN-]', sequence):
raise ValueError("Sequence contains invalid DNA characters - "
"only standard IUPAC nucleotide codes allowed")
return sequence.translate( DNA_COMPLEMENT )
def reverseComplement( sequence ):
"""
Return the reverse-complement of a sequence
NOTE: This only currently supports DNA
"""
return complement(sequence)[::-1]
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