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src/c/o/cogent-1.5.3/cogent/evolve/best_likelihood.py   cogent(Download)
        kwargs = {}
 
    aln = LoadSeqs(data=aln.todict(), **kwargs)
    columns = aligned_columns_to_rows(aln, motif_length, exclude_chars,
                                        allowed_chars)

src/p/y/pycogent-HEAD/cogent/evolve/best_likelihood.py   pycogent(Download)
        kwargs = {}
 
    aln = LoadSeqs(data=aln.todict(), **kwargs)
    columns = aligned_columns_to_rows(aln, motif_length, exclude_chars,
                                        allowed_chars)

src/p/y/pycogent-HEAD/tests/test_evolve/test_likelihood_function.py   pycogent(Download)
    def test_no_seq_named_root(self):
        """root is a reserved name"""
        aln = self.alignment.takeSeqs(self.alignment.Names[:4])
        aln = aln.todict()
        one = aln.pop(aln.keys()[0])

src/p/y/pycogent-HEAD/tests/test_core/test_core_standalone.py   pycogent(Download)
    def test_getasdict(self):
        """getting the alignment as a dictionary"""
        seqs={'seq1': 'ACGT--GT', 'seq2': 'ACGTACGT', 'seq3': 'ACGTACGT'}
        alignment = LoadSeqs(data=seqs)
        align_dict = alignment.todict()

src/c/o/cogent-1.5.3/tests/test_evolve/test_likelihood_function.py   cogent(Download)
    def test_no_seq_named_root(self):
        """root is a reserved name"""
        aln = self.alignment.takeSeqs(self.alignment.Names[:4])
        aln = aln.todict()
        one = aln.pop(aln.keys()[0])

src/c/o/cogent-1.5.3/tests/test_core/test_core_standalone.py   cogent(Download)
    def test_getasdict(self):
        """getting the alignment as a dictionary"""
        seqs={'seq1': 'ACGT--GT', 'seq2': 'ACGTACGT', 'seq3': 'ACGTACGT'}
        alignment = LoadSeqs(data=seqs)
        align_dict = alignment.todict()