Python read Examples

Example #1

File: test_phylip_io.py Project: SaswatiSadual/NPLB

 def test_parse_phylip_test_5(self):
     f = testdata_stream('phylip_test_5.phy')
     seqs = phylip_io.read(f)
     self.assertEquals(len(seqs), 6)
     self.assertEquals(len(seqs[0]), 50)
     self.assertEquals(str(seqs[1]), "GTGGTGGTGGGCGCCGGCCGTGTGGGTGGTGGTGGGCGCCGGCCGTGTGG")
     self.assertEquals(seqs[2].name, "ddrasa")

Example #2

File: test_phylip_io.py Project: SaswatiSadual/NPLB

 def test_read(self) :
     f = testdata_stream("phylip_test_1.phy")
     seqs = phylip_io.read(f)
     #print seqs
     self.assertEquals(len(seqs), 10)
     self.assertEquals(seqs[0].name, "Cow")
     self.assertEquals(len(seqs[1]), 234)

Example #3

File: test_phylip_io.py Project: SaswatiSadual/NPLB

 def test_parse_phylip_test_3(self):
     f = testdata_stream('phylip_test_3.phy')
     seqs = phylip_io.read(f)
     self.assertEquals(len(seqs), 6)
     self.assertEquals(len(seqs[0]), 20)
     self.assertEquals(str(seqs[1]), "CGTTACTCGTTGTCGTTACT")
     self.assertEquals(seqs[1].name, "Hesperorni")

Example #4

File: test_phylip_io.py Project: snehamitra/NPLB

 def test_parse_phylip_test_4(self):
     f = testdata_stream('phylip_test_4.phy')
     seqs = phylip_io.read(f)
     self.assertEquals(len(seqs), 6)
     self.assertEquals(len(seqs[0]), 25)
     self.assertEquals(str(seqs[1]), "GTGGTGGTGGGCGCCGGCCGTGTGG")
     self.assertEquals(seqs[2].name, "ddrasa")

Example #5

File: test_phylip_io.py Project: SaswatiSadual/NPLB

 def test_parse_phylip_dna(self):
     f = testdata_stream('dna.phy')
     seqs = phylip_io.read(f)
     self.assertEquals(len(seqs), 10)
     self.assertEquals(len(seqs[0]), 705)
     self.assertEquals( str(seqs[1][0:10]), "ATGGCACACC")
     self.assertEquals(seqs[2].name, "Chicken")

Example #6

File: test_phylip_io.py Project: snehamitra/NPLB

 def test_parse_phylip_test_3(self):
     f = testdata_stream('phylip_test_3.phy')
     seqs = phylip_io.read(f)
     self.assertEquals(len(seqs), 6)
     self.assertEquals(len(seqs[0]), 20)
     self.assertEquals(str(seqs[1]), "CGTTACTCGTTGTCGTTACT")
     self.assertEquals(seqs[1].name, "Hesperorni")

Example #7

File: test_phylip_io.py Project: snehamitra/NPLB

 def test_read(self):
     f = testdata_stream("phylip_test_1.phy")
     seqs = phylip_io.read(f)
     #print seqs
     self.assertEquals(len(seqs), 10)
     self.assertEquals(seqs[0].name, "Cow")
     self.assertEquals(len(seqs[1]), 234)

Example #8

File: test_phylip_io.py Project: snehamitra/NPLB

 def test_parse_phylip_dna(self):
     f = testdata_stream('dna.phy')
     seqs = phylip_io.read(f)
     self.assertEquals(len(seqs), 10)
     self.assertEquals(len(seqs[0]), 705)
     self.assertEquals(str(seqs[1][0:10]), "ATGGCACACC")
     self.assertEquals(seqs[2].name, "Chicken")

Example #9

File: test_phylip_io.py Project: ghuls/weblogo

 def test_parse_phylip_test_4(self):
     f = testdata_stream('phylip_test_4.phy')
     seqs = phylip_io.read(f)
     self.assertEqual(len(seqs), 6)
     self.assertEqual(len(seqs[0]), 25)
     self.assertEqual(str(seqs[1]), "GTGGTGGTGGGCGCCGGCCGTGTGG")
     self.assertEqual(seqs[2].name, "ddrasa")
     f.close()

Example #10

File: test_phylip_io.py Project: SLeviyang/lassie

 def test_parse_phylip_test_5(self):
     f = testdata_stream('phylip_test_5.phy')
     seqs = phylip_io.read(f)
     self.assertEqual(len(seqs), 6)
     self.assertEqual(len(seqs[0]), 50)
     self.assertEqual(str(seqs[1]), "GTGGTGGTGGGCGCCGGCCGTGTGGGTGGTGGTGGGCGCCGGCCGTGTGG")
     self.assertEqual(seqs[2].name, "ddrasa")
     f.close()