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src/c/o/cogent-1.5.3/cogent/evolve/coevolution.py   cogent(Download)
from cogent import LoadSeqs, LoadTree, PROTEIN, RNA
from cogent.core.tree import TreeError
from cogent.core.alignment import seqs_from_fasta, DenseAlignment
from cogent.parse.newick import TreeParseError
from cogent.parse.record import RecordError

src/p/y/pycogent-HEAD/cogent/evolve/coevolution.py   pycogent(Download)
from cogent import LoadSeqs, LoadTree, PROTEIN, RNA
from cogent.core.tree import TreeError
from cogent.core.alignment import seqs_from_fasta, DenseAlignment
from cogent.parse.newick import TreeParseError
from cogent.parse.record import RecordError

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_seqs_from_fasta(self):
        """seqs_from_fasta should initialize seqs from fasta-format string"""
        s = '>aa\nAB\nC\n>bb\nDE\nF\n'
        obs_a, obs_labels = seqs_from_fasta(s)
        self.assertEqual(obs_a, ['ABC','DEF'])

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_seqs_from_fasta(self):
        """seqs_from_fasta should initialize seqs from fasta-format string"""
        s = '>aa\nAB\nC\n>bb\nDE\nF\n'
        obs_a, obs_labels = seqs_from_fasta(s)
        self.assertEqual(obs_a, ['ABC','DEF'])