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))