Back to index

python-biopython  1.60
Public Member Functions | Public Attributes
test_Wise.TestWiseDryRun Class Reference

List of all members.

Public Member Functions

def setUp
def test_dnal
def test_psw
def tearDown

Public Attributes

 old_stdout

Detailed Description

Definition at line 18 of file test_Wise.py.


Member Function Documentation

Definition at line 19 of file test_Wise.py.

00019 
00020     def setUp(self):
00021         self.old_stdout = sys.stdout
00022         sys.stdout = cStringIO.StringIO()
        

Definition at line 37 of file test_Wise.py.

00037 
00038     def tearDown(self):
00039         sys.stdout = self.old_stdout

Call dnal, and do a trivial check on its output.

Definition at line 23 of file test_Wise.py.

00023 
00024     def test_dnal(self):
00025         """Call dnal, and do a trivial check on its output."""
00026         Wise.align(["dnal"], ("seq1.fna", "seq2.fna"), kbyte=100000, dry_run=True)
00027         #If test output is redirected to a file, the wrapper adds -quiet
00028         output = sys.stdout.getvalue().replace(" -quiet ", " ")
00029         self.assertTrue(output.startswith("dnal -kbyte 100000 seq1.fna seq2.fna"), output[:200])

Call psw, and do a trivial check on its output.

Definition at line 30 of file test_Wise.py.

00030 
00031     def test_psw(self):
00032         """Call psw, and do a trivial check on its output."""
00033         Wise.align(["psw"], ("seq1.faa", "seq2.faa"), dry_run=True, kbyte=4)
00034         #If test output is redirected to a file, the wrapper adds -quiet
00035         output = sys.stdout.getvalue().replace(" -quiet ", " ")
00036         self.assertTrue(output.startswith("psw -kbyte 4 seq1.faa seq2.faa"), output[:200])


Member Data Documentation

Definition at line 20 of file test_Wise.py.


The documentation for this class was generated from the following file: