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src/c/o/cogent-1.5.3/tests/test_core/test_alignment.py   cogent(Download)
from cogent.struct.rna2d import ViennaStructure
 
from cogent.core.alignment import SequenceCollection, \
    make_gap_filter, coerce_to_string, \
    seqs_from_array, seqs_from_model_seqs, seqs_from_generic, seqs_from_fasta, \
    def test_aln_from_collection(self):
        """aln_from_collection should initialize from existing alignment"""
        a = SequenceCollection(['AAA','GGG'])
        obs_a, obs_labels = aln_from_collection(a, Alphabet=RNA.Alphabet)
        self.assertEqual(a.toFasta(), '>seq_0\nAAA\n>seq_1\nGGG')

src/p/y/pycogent-HEAD/tests/test_core/test_alignment.py   pycogent(Download)
from cogent.struct.rna2d import ViennaStructure
 
from cogent.core.alignment import SequenceCollection, \
    make_gap_filter, coerce_to_string, \
    seqs_from_array, seqs_from_model_seqs, seqs_from_generic, seqs_from_fasta, \
    def test_aln_from_collection(self):
        """aln_from_collection should initialize from existing alignment"""
        a = SequenceCollection(['AAA','GGG'])
        obs_a, obs_labels = aln_from_collection(a, Alphabet=RNA.Alphabet)
        self.assertEqual(a.toFasta(), '>seq_0\nAAA\n>seq_1\nGGG')