def __init__(self, records="", name=None, alphabet=default_codon_alphabet):
MultipleSeqAlignment.__init__(self, records, alphabet=alphabet)
# check the type of the alignment to be nucleotide
for rec in self:
if not isinstance(rec.seq, CodonSeq):
raise TypeError("CodonSeq objects are expected in each " "SeqRecord in CodonAlignment")
assert self.get_alignment_length() % 3 == 0, "Alignment length is not a triple number"
def __init__(self, records='', name=None, alphabet=default_codon_alphabet):
MultipleSeqAlignment.__init__(self, records, alphabet=alphabet)
# check the type of the alignment to be nucleotide
for rec in self:
if not isinstance(rec.seq, CodonSeq):
raise TypeError("CodonSeq objects are expected in each "
"SeqRecord in CodonAlignment")
assert self.get_alignment_length() % 3 == 0, \
"Alignment length is not a triple number"
def __init__(self, records='', name=None, alphabet=default_codon_alphabet):
"""Initialize the class."""
MultipleSeqAlignment.__init__(self, records, alphabet=alphabet)
# check the type of the alignment to be nucleotide
for rec in self:
if not isinstance(rec.seq, CodonSeq):
raise TypeError("CodonSeq objects are expected in each "
"SeqRecord in CodonAlignment")
if self.get_alignment_length() % 3 != 0:
raise ValueError("Alignment length is not a multiple of "
"three (i.e. a whole number of codons)")
def __init__(self, records='', name=None, alphabet=default_codon_alphabet):
"""Initialize the class."""
MultipleSeqAlignment.__init__(self, records, alphabet=alphabet)
# check the type of the alignment to be nucleotide
for rec in self:
if not isinstance(rec.seq, CodonSeq):
raise TypeError("CodonSeq objects are expected in each "
"SeqRecord in CodonAlignment")
if self.get_alignment_length() % 3 != 0:
raise ValueError("Alignment length is not a multiple of "
"three (i.e. a whole number of codons)")
def __init__(self, records,
# CMA-specific attributes here
# one=1,
level=0,
name=None,
params=None,
query_length=None,
query_chars=None,
):
# NB: alphabet is always protein; X is OK
MultipleSeqAlignment.__init__(self, records, extended_protein)
self.level = level
self.name = name
self.params = params
self.query_length = query_length
self.query_chars = query_chars
def __init__(
self,
records,
# CMA-specific attributes here
# one=1,
level=0,
name=None,
params=None,
query_length=None,
query_chars=None,
):
# NB: alphabet is always protein; X is OK
MultipleSeqAlignment.__init__(self, records, extended_protein)
self.level = level
self.name = name
self.params = params
self.query_length = query_length
self.query_chars = query_chars
def __init__(self, records, alphabet=None, annotations=None):
MultipleSeqAlignment.__init__(self, records, alphabet, annotations)
self._db = dict((self[i].id, i) for i in xrange(len(self)))
def __init__(self, records, alphabet=None, annotations=None):
MultipleSeqAlignment.__init__(self, records, alphabet, annotations)
self._db = dict((self[i].id, i) for i in xrange(len(self)))
