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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):
        """RNAsubopt: BaseCommand should be ok for different parameter settings
        """
        r = RNAsubopt()
        obs = r.BaseCommand.split()
        temp_dir = tempfile.mkdtemp()
        #changing in initialization
        r = RNAsubopt(WorkingDir=temp_dir)
        self.assertEqual(r.BaseCommand,\
            'cd "%s/"; RNAsubopt -e 1 -d2 -T 37'%(temp_dir))
        #changing afterwards
        r = RNAsubopt()
    def test_stdout(self):
        """RNAsubopt: StdOut should be as expected"""
        r = RNAsubopt()
        seq = ['AUAGCUAGCUAUGCGCUAGCGGAUUAGCUAGCUAGCGA',\
        'ucgaucgaucagcuagcuauuauauaua']

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):
        """RNAsubopt: BaseCommand should be ok for different parameter settings
        """
        r = RNAsubopt()
        obs = r.BaseCommand.split()
        temp_dir = tempfile.mkdtemp()
        #changing in initialization
        r = RNAsubopt(WorkingDir=temp_dir)
        self.assertEqual(r.BaseCommand,\
            'cd "%s/"; RNAsubopt -e 1 -d2 -T 37'%(temp_dir))
        #changing afterwards
        r = RNAsubopt()
    def test_stdout(self):
        """RNAsubopt: StdOut should be as expected"""
        r = RNAsubopt()
        seq = ['AUAGCUAGCUAUGCGCUAGCGGAUUAGCUAGCUAGCGA',\
        'ucgaucgaucagcuagcuauuauauaua']