def test_simple_phylo_inference ( self ) :
"""
Test of the phylogenetic inference method for all the available
configurations with supported input and output formats.
"""
for keyword in viewkeys(Inference.get_keywords(raxml_exe)) :
self.standard_test('fasta', '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 phylogenetic inference tool.
"""
infile = '{}/f001.mafft_default.aln'.format(informat.capitalize())
outfile = 'tmp_test.tree'
self.add_file_to_clean(outfile)
# Check the input
self.assertTrue(os.path.isfile(infile))
self.assertEqual(len(list(SeqIO.parse(infile, informat))), 50)
# Generate the phylogeny
t, score = Inference.get_phylogeny(fasttree_exe,
infile,
informat,
args=params,
outfile=outfile,
outfile_format=outformat)
# Check the output
self.assertTrue(os.path.isfile(outfile))
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 phylogenetic inference tool.
"""
infile = '{}/f001.mafft_default.aln'.format(informat.capitalize())
outfile = 'tmp_test.tree'
self.add_file_to_clean(outfile)
# Check the input
self.assertTrue(os.path.isfile(infile))
self.assertEqual(len(list(SeqIO.parse(infile, informat))), 50)
# Generate the phylogeny
t, score = Inference.get_phylogeny(raxml_exe, infile, informat,
args=params, outfile=outfile, outfile_format=outformat)
# Check the output
self.assertTrue(os.path.isfile(outfile))
