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python-biopython  1.60
Public Member Functions | Public Attributes
test_NCBITextParser.TestBlastRecord Class Reference

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Public Member Functions

def setUp
def test_conversion

Public Attributes

 parser

Detailed Description

Definition at line 12 of file test_NCBITextParser.py.


Member Function Documentation

Definition at line 16 of file test_NCBITextParser.py.

00016 
00017     def setUp(self):
00018         self.parser = NCBIStandalone.BlastParser()

Definition at line 19 of file test_NCBITextParser.py.

00019 
00020     def test_conversion(self):
00021         "Test converting a Blast record multiple alignment"
00022 
00023         from Bio.Alphabet import IUPAC
00024 
00025         path = os.path.join("Blast", 'bt005.txt')
00026         handle = open(path)
00027         record = self.parser.parse(handle)
00028         handle.close()
00029         generic_align = record.multiple_alignment.to_generic(IUPAC.protein)
00030         test_seq = generic_align[0].seq
00031         self.assertEqual(test_seq.alphabet, IUPAC.protein)
00032         self.assertEqual(test_seq[:60].tostring(), record.multiple_alignment.alignment[0][2])
00033 

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Member Data Documentation

Definition at line 17 of file test_NCBITextParser.py.


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