Back to index

python-biopython  1.60
Public Member Functions | Public Attributes
test_EmbossPrimer.PrimersearchParseTest Class Reference

List of all members.

Public Member Functions

def setUp
def test_simple_parse
def test_in_depth_normal_parse

Public Attributes

 test_files

Detailed Description

Definition at line 185 of file test_EmbossPrimer.py.


Member Function Documentation

Definition at line 186 of file test_EmbossPrimer.py.

00186 
00187     def setUp(self):
00188         self.test_files = \
00189           [os.path.join("Emboss", "bac_find.psearch")]

Make sure the output from a simple primersearch file is correct.

Definition at line 198 of file test_EmbossPrimer.py.

00198 
00199     def test_in_depth_normal_parse(self):
00200         """Make sure the output from a simple primersearch file is correct.
00201         """
00202         file = self.test_files[0]
00203         h = open(file, "r")
00204         amp_info = PrimerSearch.read(h)
00205         h.close()
00206 
00207         self.assertEqual(len(amp_info.amplifiers), 1)
00208         self.assertTrue("Test" in amp_info.amplifiers)
00209         self.assertEqual(len(amp_info.amplifiers["Test"]), 1)
00210 
00211         self.assertEqual(amp_info.amplifiers["Test"][0].length, 218)
00212         self.assertEqual(amp_info.amplifiers["Test"][0].hit_info,
00213           "AC074298 AC074298 \n"
00214           "\tTelomere associated sequence for Arabidopsis thaliana "
00215           "TEL1N from chromosome I, complete sequence.\n"
00216           "\tCCGGTTTCTCTGGTTGAAAA hits forward strand at 114 with "
00217           "0 mismatches\n"
00218           "\tTCACATTCCCAAATGTAGATCG hits reverse strand at [114] with "
00219           "0 mismatches")

Here is the call graph for this function:

Make sure that we can parse all primersearch files.

Definition at line 190 of file test_EmbossPrimer.py.

00190 
00191     def test_simple_parse(self):
00192         """Make sure that we can parse all primersearch files.
00193         """
00194         for file in self.test_files:
00195             h = open(file, "r")
00196             PrimerSearch.read(h)
00197             h.close()

Here is the call graph for this function:


Member Data Documentation

Definition at line 187 of file test_EmbossPrimer.py.


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