Did I find the right examples for you? yes no

All Samples(6)  |  Call(0)  |  Derive(0)  |  Import(6)

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,\
            char_order = "ABC"           
        elif al is a: #need protein_order   
            char_order=PROTEIN_ORDER
        else: #need DNA_order
            char_order=DNA_ORDER

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,\
            char_order = "ABC"           
        elif al is a: #need protein_order   
            char_order=PROTEIN_ORDER
        else: #need DNA_order
            char_order=DNA_ORDER

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,\

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,\

src/p/y/pycogent-HEAD/tests/test_align/test_weights/test_methods.py   pycogent(Download)
from cogent.core.alignment import Alignment
from cogent.core.profile import Profile
from cogent.align.weights.util import DNA_ORDER, PROTEIN_ORDER
from cogent.align.weights.methods import VA, VOR, mVOR, pos_char_weights, PB,\
    SS, ACL, GSC, _clip_branch_lengths, _set_branch_sum, _set_node_weight
    def test_pos_char_weights(self):
        """pos_char_weights: should return correct contributions at each pos
        """
        #build expected profile
        exp_data = zeros([len(PROTEIN_ORDER),self.aln2.SeqLen],Float64)
            for k,v in weights.items():
                exp_data[PROTEIN_ORDER.index(k),pos] = v
        exp_aln2 = Profile(exp_data,Alphabet=PROTEIN_ORDER)
 
        #check observed against expected

src/c/o/cogent-1.5.3/tests/test_align/test_weights/test_methods.py   cogent(Download)
from cogent.core.alignment import Alignment
from cogent.core.profile import Profile
from cogent.align.weights.util import DNA_ORDER, PROTEIN_ORDER
from cogent.align.weights.methods import VA, VOR, mVOR, pos_char_weights, PB,\
    SS, ACL, GSC, _clip_branch_lengths, _set_branch_sum, _set_node_weight
    def test_pos_char_weights(self):
        """pos_char_weights: should return correct contributions at each pos
        """
        #build expected profile
        exp_data = zeros([len(PROTEIN_ORDER),self.aln2.SeqLen],Float64)
            for k,v in weights.items():
                exp_data[PROTEIN_ORDER.index(k),pos] = v
        exp_aln2 = Profile(exp_data,Alphabet=PROTEIN_ORDER)
 
        #check observed against expected