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src/c/o/cogent-1.5.3/cogent/format/motif.py   cogent(Download)
from cogent.util.dict2d import Dict2D
from numpy import zeros, nonzero
from cogent.align.weights.util import AlnToProfile
from zipfile import ZipFile
from cogent.app.util import get_tmp_filename
                curr_id = module.ID
                conserved_positions[curr_id]=[]
                curr_profile = AlnToProfile(module,self.MotifResults.MolType)
                for ix,pos in enumerate(curr_profile.rowMax()):
                    if pos >= min_conservation:

src/p/y/pycogent-HEAD/cogent/format/motif.py   pycogent(Download)
from cogent.util.dict2d import Dict2D
from numpy import zeros, nonzero
from cogent.align.weights.util import AlnToProfile
from zipfile import ZipFile
from cogent.app.util import get_tmp_filename
                curr_id = module.ID
                conserved_positions[curr_id]=[]
                curr_profile = AlnToProfile(module,self.MotifResults.MolType)
                for ix,pos in enumerate(curr_profile.rowMax()):
                    if pos >= min_conservation:

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,\