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, # 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)))