def maskSequences(sequences, masker=None):
'''return a list of masked sequence.
*masker* can be one of
dust/dustmasker * run dustmasker on sequences
softmask * use softmask to hardmask sequences
'''
if masker in ("dust", "dustmasker"):
masker_object = Masker.MaskerDustMasker()
else:
masker_object = None
if masker == "softmask":
# the genome sequence is repeat soft-masked
masked_seq = sequences
elif masker in ("dust", "dustmasker"):
# run dust
masked_seq = masker_object.maskSequences(
[x.upper() for x in sequences])
elif masker is None:
masked_seq = [x.upper() for x in sequences]
else:
raise ValueError("unknown masker %s" % masker)
# hard mask softmasked characters
masked_seq = [re.sub("[a-z]", "N", x) for x in masked_seq]
return masked_seq
def maskSequences(sequences, masker):
if masker == "repeatmasker":
# the genome sequence is repeat masked
masked_seq = sequences
elif masker == "dust":
masker_object = Masker.MaskerDustMasker()
masked_seq = [masker_object(x.upper()) for x in sequences]
else:
masked_seq = [x.upper() for x in sequences]
# hard mask softmasked characters
masked_seq = [re.sub("[a-z]", "N", x) for x in masked_seq]
return masked_seq
class DustMaskerCheck(unittest.TestCase):
mMasker = Masker.MaskerDustMasker()