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src/c/o/cogent-1.5.3/cogent/align/weights/methods.py   cogent(Download)
from cogent.parse.tree import DndParser
from cogent.util.array import hamming_distance
from cogent.align.weights.util import Weights, number_of_pseudo_seqs,\
    pseudo_seqs_exact, pseudo_seqs_monte_carlo, row_to_vote, distance_matrix,\
    eigenvector_for_largest_eigenvalue, DNA_ORDER,RNA_ORDER,PROTEIN_ORDER,\
 
    #create a dictionary of {seq_id: weight}
    weight_dict = Weights(dict(zip(alignment.Names,weights)))
    return weight_dict
 
        votes = row_to_vote(array(temp)) #change distances to votes
        weights += votes #add to previous weights
    weight_dict = Weights(dict(zip(aln_array.Names,weights)))
    weight_dict.normalize() #normalize
 
        votes = row_to_vote(array(temp))
        weights += votes
    weight_dict = Weights(dict(zip(alignment.Names,weights)))
    weight_dict.normalize()
    return weight_dict
    d = pos_weights.Data
 
    result = Weights()
 
    for key,seq in alignment.items():

src/p/y/pycogent-HEAD/cogent/align/weights/methods.py   pycogent(Download)
from cogent.parse.tree import DndParser
from cogent.util.array import hamming_distance
from cogent.align.weights.util import Weights, number_of_pseudo_seqs,\
    pseudo_seqs_exact, pseudo_seqs_monte_carlo, row_to_vote, distance_matrix,\
    eigenvector_for_largest_eigenvalue, DNA_ORDER,RNA_ORDER,PROTEIN_ORDER,\
 
    #create a dictionary of {seq_id: weight}
    weight_dict = Weights(dict(zip(alignment.Names,weights)))
    return weight_dict
 
        votes = row_to_vote(array(temp)) #change distances to votes
        weights += votes #add to previous weights
    weight_dict = Weights(dict(zip(aln_array.Names,weights)))
    weight_dict.normalize() #normalize
 
        votes = row_to_vote(array(temp))
        weights += votes
    weight_dict = Weights(dict(zip(alignment.Names,weights)))
    weight_dict.normalize()
    return weight_dict
    d = pos_weights.Data
 
    result = Weights()
 
    for key,seq in alignment.items():

src/c/o/cogent-1.5.3/tests/test_align/test_weights/test_util.py   cogent(Download)
from cogent.core.sequence import DnaSequence, RnaSequence
from cogent.core.moltype import DNA, RNA
from cogent.align.weights.util import Weights, number_of_pseudo_seqs,\
    pseudo_seqs_exact, pseudo_seqs_monte_carlo, row_to_vote, distance_matrix,\
    eigenvector_for_largest_eigenvalue, DNA_ORDER,RNA_ORDER,PROTEIN_ORDER,\
    def test_weights(self):
        """Weights: should behave like a normal dict and can be normalized
        """
        w = Weights({'seq1':2, 'seq2':3, 'seq3':10})
        self.assertEqual(w['seq1'],2)

src/p/y/pycogent-HEAD/tests/test_align/test_weights/test_util.py   pycogent(Download)
from cogent.core.sequence import DnaSequence, RnaSequence
from cogent.core.moltype import DNA, RNA
from cogent.align.weights.util import Weights, number_of_pseudo_seqs,\
    pseudo_seqs_exact, pseudo_seqs_monte_carlo, row_to_vote, distance_matrix,\
    eigenvector_for_largest_eigenvalue, DNA_ORDER,RNA_ORDER,PROTEIN_ORDER,\
    def test_weights(self):
        """Weights: should behave like a normal dict and can be normalized
        """
        w = Weights({'seq1':2, 'seq2':3, 'seq3':10})
        self.assertEqual(w['seq1'],2)