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src/c/o/cogent-1.5.3/cogent/seqsim/sequence_generators.py   cogent(Download)
from cogent.maths.stats.util import Freqs
from cogent.struct.rna2d import ViennaStructure
from cogent.app.vienna_package import RNAfold
from numpy import logical_and, fromstring, byte
 
            positions.append(curr_positions)
            seqs.append(curr_seq)
        folder = RNAfold(params={'-T':temp})
        struct_file = folder(seqs)['StdOut']
        odd = False

src/p/y/pycogent-HEAD/cogent/seqsim/sequence_generators.py   pycogent(Download)
from cogent.maths.stats.util import Freqs
from cogent.struct.rna2d import ViennaStructure
from cogent.app.vienna_package import RNAfold
from numpy import logical_and, fromstring, byte
 
            positions.append(curr_positions)
            seqs.append(curr_seq)
        folder = RNAfold(params={'-T':temp})
        struct_file = folder(seqs)['StdOut']
        odd = False

src/c/o/cogent-1.5.3/tests/test_app/test_vienna_package.py   cogent(Download)
import tempfile, shutil
from cogent.util.unit_test import TestCase, main
from cogent.app.vienna_package import RNAfold, RNAsubopt, RNAplot,\
    plot_from_seq_and_struct, DataError, get_constrained_fold, \
    get_secondary_structure
    def test_base_command(self):
        """RNAfold: BaseCommand should be ok for different parameter settings"""
        r = RNAfold()
        working_dir = getcwd()
 
    def test_changing_working_dir(self):
        """RNAfold: BaseCommand should be ok after changing the working dir"""
        #changing in initialization
        temp_dir = tempfile.mkdtemp()
        r = RNAfold(WorkingDir=temp_dir)
        self.assertEqual(r.BaseCommand,\
            'cd "%s/"; RNAfold -d1 -T 37 -S 1.07'%(temp_dir))
        #changing afterwards
        r = RNAfold()
    def test_stdout(self):
        """RNAfold: StdOut should be as expected"""
        r = RNAfold()
        exp = '\n'.join(['>namedseq1','AUAGCUAGCUAUGCGCUAGC',\
            '...((((((.....)))))) ( -8.30)','ACGGCUAUAGCUAGCGA',\

src/p/y/pycogent-HEAD/tests/test_app/test_vienna_package.py   pycogent(Download)
import tempfile, shutil
from cogent.util.unit_test import TestCase, main
from cogent.app.vienna_package import RNAfold, RNAsubopt, RNAplot,\
    plot_from_seq_and_struct, DataError, get_constrained_fold, \
    get_secondary_structure
    def test_base_command(self):
        """RNAfold: BaseCommand should be ok for different parameter settings"""
        r = RNAfold()
        working_dir = getcwd()
 
    def test_changing_working_dir(self):
        """RNAfold: BaseCommand should be ok after changing the working dir"""
        #changing in initialization
        temp_dir = tempfile.mkdtemp()
        r = RNAfold(WorkingDir=temp_dir)
        self.assertEqual(r.BaseCommand,\
            'cd "%s/"; RNAfold -d1 -T 37 -S 1.07'%(temp_dir))
        #changing afterwards
        r = RNAfold()
    def test_stdout(self):
        """RNAfold: StdOut should be as expected"""
        r = RNAfold()
        exp = '\n'.join(['>namedseq1','AUAGCUAGCUAUGCGCUAGC',\
            '...((((((.....)))))) ( -8.30)','ACGGCUAUAGCUAGCGA',\