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src/c/o/cogent-1.5.3/tests/test_app/test_clustalw.py   cogent(Download)
from cogent.util.unit_test import TestCase, main
from cogent.util.misc import flatten
from cogent.app.clustalw import Clustalw, alignUnalignedSeqsFromFile,\
    alignUnalignedSeqs, alignTwoAlignments, addSeqsToAlignment,\
    buildTreeFromAlignment, build_tree_from_alignment, \
    def test_base_command(self):
        """Clustalw BaseCommand should return the correct BaseCommand"""
        c = Clustalw()
        self.assertEqual(c.BaseCommand,\
            ''.join(['cd "',getcwd(),'/"; ','clustalw -align']))
    def test_changing_working_dir(self):
        """Clustalw BaseCommand should change according to WorkingDir"""
        c = Clustalw(WorkingDir='/tmp/clustaltest')
        self.assertEqual(c.BaseCommand,\
            ''.join(['cd "','/tmp/clustaltest','/"; ','clustalw -align']))
        c = Clustalw(WorkingDir='/tmp/clustaltest/')
        self.assertEqual(c.BaseCommand,\
            ''.join(['cd "','/tmp/clustaltest/','/"; ','clustalw -align']))
        c = Clustalw()

src/p/y/pycogent-HEAD/tests/test_app/test_clustalw.py   pycogent(Download)
from cogent.util.unit_test import TestCase, main
from cogent.util.misc import flatten
from cogent.app.clustalw import Clustalw, alignUnalignedSeqsFromFile,\
    alignUnalignedSeqs, alignTwoAlignments, addSeqsToAlignment,\
    buildTreeFromAlignment, build_tree_from_alignment, \
    def test_base_command(self):
        """Clustalw BaseCommand should return the correct BaseCommand"""
        c = Clustalw()
        self.assertEqual(c.BaseCommand,\
            ''.join(['cd "',getcwd(),'/"; ','clustalw -align']))
    def test_changing_working_dir(self):
        """Clustalw BaseCommand should change according to WorkingDir"""
        c = Clustalw(WorkingDir='/tmp/clustaltest')
        self.assertEqual(c.BaseCommand,\
            ''.join(['cd "','/tmp/clustaltest','/"; ','clustalw -align']))
        c = Clustalw(WorkingDir='/tmp/clustaltest/')
        self.assertEqual(c.BaseCommand,\
            ''.join(['cd "','/tmp/clustaltest/','/"; ','clustalw -align']))
        c = Clustalw()