def test_simple_phylo_assembly ( self ) :
"""
Test of the consensus tree method for all the available configurations
with supported input and output formats.
"""
for keyword in viewkeys(PhyloAssemble.get_keywords(consense_exe)) :
self.standard_test('newick', 'newick', keyword)
def standard_test ( self, informat, outformat, params ) :
"""
Standard testing procedure used by all tests.
Arguments :
informat ( string )
Input file format.
outformat ( string )
Output file format.
params ( string )
Arguments passed to the consensus tree tool.
"""
infile = '{}/f002.trees.{}'.format(informat.capitalize(), informat)
outfile = 'tmp_test.tree'
self.add_file_to_clean(outfile)
# Check the input
self.assertTrue(os.path.isfile(infile))
self.assertEqual(len(list(Phylo.parse(infile, informat))), 9)
# Generate the consensus tree
PhyloAssemble.get_consensus_tree(consense_exe, infile, informat,
args=params, outfile=outfile, outfile_format=outformat)
# Check the output
self.assertTrue(os.path.isfile(outfile))