Python Alignment Examples

Example #1

File: test.py Project: kgori/treeCl

 def test_read_bzip2_fasta_file(self):
     filename = os.path.join(thisdir, 'data', 'mini', 'class1_1.fas.bz2')
     al = Alignment(filename, 'fasta')
     expected = ['Sp1', 'Sp2', 'Sp3', 'Sp4', 'Sp5']
     self.assertListEqual(expected, al.get_names())

Example #2

File: test.py Project: kgori/treeCl

 def test_read_gzip_phylip_file(self):
     filename = os.path.join(thisdir, 'data', 'mini', 'class1_1.phy.gz')
     al = Alignment(filename, 'phylip')
     expected = ['Sp1', 'Sp2', 'Sp3', 'Sp4', 'Sp5']
     self.assertListEqual(expected, al.get_names())

Example #3

 def test_read_bzip2_fasta_file(self):
     filename = os.path.join(thisdir, 'data', 'mini', 'class1_1.fas.bz2')
     al = Alignment(filename, 'fasta')
     expected = ['Sp1', 'Sp2', 'Sp3', 'Sp4', 'Sp5']
     self.assertListEqual(expected, al.get_names())

Example #4

 def test_read_gzip_phylip_file(self):
     filename = os.path.join(thisdir, 'data', 'mini', 'class1_1.phy.gz')
     al = Alignment(filename, 'phylip')
     expected = ['Sp1', 'Sp2', 'Sp3', 'Sp4', 'Sp5']
     self.assertListEqual(expected, al.get_names())

Example #5

File: test.py Project: kgori/treeCl

 def test_read_bzip2_fasta_file(self):
     filename = os.path.join(thisdir, "data", "mini", "class1_1.fas.bz2")
     al = Alignment(filename, "fasta")
     expected = ["Sp1", "Sp2", "Sp3", "Sp4", "Sp5"]
     self.assertListEqual(expected, al.get_names())

Example #6

File: test.py Project: kgori/treeCl

 def test_read_gzip_phylip_file(self):
     filename = os.path.join(thisdir, "data", "mini", "class1_1.phy.gz")
     al = Alignment(filename, "phylip")
     expected = ["Sp1", "Sp2", "Sp3", "Sp4", "Sp5"]
     self.assertListEqual(expected, al.get_names())