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python-biopython  1.60
Public Member Functions | Public Attributes
test_NNGene.SignatureFinderTest Class Reference

List of all members.

Public Member Functions

def setUp
def test_find

Public Attributes

 test_records
 sig_finder

Detailed Description

Test the ability to find signatures in a set of sequences.

Definition at line 583 of file test_NNGene.py.


Member Function Documentation

Definition at line 586 of file test_NNGene.py.

00586 
00587     def setUp(self):
00588         test_file = os.path.join('NeuralNetwork', 'enolase.fasta')
00589 
00590         self.test_records = []
00591 
00592         # load the records
00593         handle = open(test_file, 'r')
00594         self.test_records = list(SeqIO.parse(handle, "fasta",
00595                                              alphabet=IUPAC.unambiguous_dna))
00596         handle.close()
00597 
00598         self.sig_finder = Signature.SignatureFinder()

Find signatures from sequence inputs.

Definition at line 599 of file test_NNGene.py.

00599 
00600     def test_find(self):
00601         """Find signatures from sequence inputs.
00602         """
00603         repository = self.sig_finder.find(self.test_records, 6, 9)
00604         top_sig = repository.get_top(1)
00605 
00606         assert top_sig[0] == ('TTGGAA', 'TGGAAA'), \
00607                "Unexpected signature %s" % top_sig[0]


Member Data Documentation

Definition at line 597 of file test_NNGene.py.

Definition at line 589 of file test_NNGene.py.


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