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#################################################################################
# Copyright (c) 2011-2015, Pacific Biosciences of California, Inc.
#
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright
# notice, this list of conditions and the following disclaimer in the
# documentation and/or other materials provided with the distribution.
# * Neither the name of Pacific Biosciences nor the names of its
# contributors may be used to endorse or promote products derived from
# this software without specific prior written permission.
#
# NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY
# THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC BIOSCIENCES AND ITS
# CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR
# ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
# BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER
# IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
#################################################################################
# sequence.py: module of basic sequence methods
# Authors: Brett Bowman, David Alexander
__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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