Back to index

python-biopython  1.60
Public Member Functions
test_Wise.TestWise Class Reference

List of all members.

Public Member Functions

def test_align

Detailed Description

Definition at line 40 of file test_Wise.py.


Member Function Documentation

Call dnal with optional arguments, and do a trivial check on the output.

Definition at line 41 of file test_Wise.py.

00041 
00042     def test_align(self):
00043         """Call dnal with optional arguments, and do a trivial check on the output."""
00044         temp_file = Wise.align(["dnal"], ("Wise/human_114_g01_exons.fna_01", "Wise/human_114_g02_exons.fna_01"), kbyte=100000, force_type="DNA", quiet=True)
00045         line = temp_file.readline().rstrip()
00046         if line == "Score 114":
00047             #Wise 2.4.1 includes a score line, even in quiet mode, ignore this
00048             line = temp_file.readline().rstrip()
00049         if line == "ENSG00000172135   AGGGAAAGCCCCTAAGCTC--CTGATCTATGCTGCATCCAGTTTGCAAAGTGGGGTCCC":
00050             #This is what we expect from wise 2.2.0 (and earlier)
00051             pass
00052         elif line == "ENSG00000172135   AGGGAAAGCCCCTAAGCTC--CTGATCTATGCTGCATCCAGTTTGCAAAG-TGGGGTCC":
00053             #This is what we expect from wise 2.4.1
00054             pass
00055         else:
00056             #Bad!
00057             self.assertTrue(False, line)
00058 


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