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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):
        """RNAplot: BaseCommand should be ok for different parameter settings"""
        r = RNAplot()
        working_dir = getcwd()
        self.assertEqual(r.BaseCommand,\
    def test_changing_working_dir(self):
        """RNAplot: BaseCommand should be ok after changing the working dir"""
        #changing in initialization
        temp_dir = tempfile.mkdtemp()
        r = RNAplot(WorkingDir=temp_dir)
        self.assertEqual(r.BaseCommand,\
            'cd "%s/"; RNAplot'%(temp_dir))
        #changing afterwards
        r = RNAplot()
    def test_get_result_paths_unnamed_seq(self):
        """RNAplot: _get_result_paths() should work on unnamed seq"""
        r = RNAplot()
        res = r(self.unnamed_seqs)
        self.assertEqualItems(res.keys(),\

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):
        """RNAplot: BaseCommand should be ok for different parameter settings"""
        r = RNAplot()
        working_dir = getcwd()
        self.assertEqual(r.BaseCommand,\
    def test_changing_working_dir(self):
        """RNAplot: BaseCommand should be ok after changing the working dir"""
        #changing in initialization
        temp_dir = tempfile.mkdtemp()
        r = RNAplot(WorkingDir=temp_dir)
        self.assertEqual(r.BaseCommand,\
            'cd "%s/"; RNAplot'%(temp_dir))
        #changing afterwards
        r = RNAplot()
    def test_get_result_paths_unnamed_seq(self):
        """RNAplot: _get_result_paths() should work on unnamed seq"""
        r = RNAplot()
        res = r(self.unnamed_seqs)
        self.assertEqualItems(res.keys(),\