def test_run_raxml_ancestor_reconstruction(self):
raxml_seq_recon = RAxMLSequenceReconstruction('gubbins/tests/data/raxml_sequence_reconstruction/input_alignment.fasta',
'gubbins/tests/data/raxml_sequence_reconstruction/unrooted_tree.newick',
'outputfile', 'output_tree', RAxMLExecutable(1).internal_sequence_reconstruction_command(), False)
raxml_seq_recon.reconstruct_ancestor_sequences()
assert os.path.exists('outputfile')
def test_more_complex_tree(self):
raxml_seq_recon = RAxMLSequenceReconstruction('gubbins/tests/data/multiple_recombinations.aln',
'gubbins/tests/data/expected_RAxML_result.multiple_recombinations.iteration_5.output_tree',
'output_alignment', 'output_tree', RAxMLExecutable(1).internal_sequence_reconstruction_command(), False)
raxml_seq_recon.reconstruct_ancestor_sequences()
assert os.path.exists('output_alignment')
assert os.path.exists('output_tree')
def test_transfer_internal_labels(self):
raxml_seq_recon = RAxMLSequenceReconstruction('', '', '', 'output_tree', '', False)
raxml_seq_recon.transfer_internal_names_to_tree('gubbins/tests/data/source_tree.tre', 'gubbins/tests/data/destination_tree.tre', 'renamed_output_tree')
assert os.path.exists('renamed_output_tree')
self.assertTrue(filecmp.cmp('renamed_output_tree','gubbins/tests/data/expected_renamed_output_tree', shallow = False))
def test_add_labels_to_tree(self):
raxml_seq_recon = RAxMLSequenceReconstruction('', '', '', '', '', False)
raxml_seq_recon.root_tree('gubbins/tests/data/raxml_sequence_reconstruction/unrooted_tree.newick', raxml_seq_recon.temp_rooted_tree)
tree = dendropy.Tree.get_from_path(raxml_seq_recon.temp_rooted_tree, 'newick', preserve_underscores=True)
self.assertEqual("((B:0.1,(C:0.1,(D:0.1,E:0.1))),(A:0.1,F:0.1):0.0);\n",tree.as_string(schema='newick'))
def test_merging_fasta_files(self):
raxml_seq_recon = RAxMLSequenceReconstruction('', '', '', '', '', False)
raxml_seq_recon.combine_fastas('gubbins/tests/data/raxml_sequence_reconstruction/1.fasta','gubbins/tests/data/raxml_sequence_reconstruction/2.fasta','combined.fasta')
self.assertTrue(filecmp.cmp('combined.fasta','gubbins/tests/data/raxml_sequence_reconstruction/expected_combined_1_2.fasta', shallow = False))
def test_convert_raw_ancestral_file_to_fasta(self):
raxml_seq_recon = RAxMLSequenceReconstruction('', '', '', '', '', False)
raxml_seq_recon.convert_raw_ancestral_states_to_fasta('gubbins/tests/data/raxml_sequence_reconstruction/raw_marginalAncestralStates.phylip','outputfile')
self.assertTrue(filecmp.cmp('outputfile','gubbins/tests/data/raxml_sequence_reconstruction/expected_marginalAncestralStates.fasta', shallow = False))
def test_root_input_tree(self):
raxml_seq_recon = RAxMLSequenceReconstruction('abc', 'gubbins/tests/data/raxml_sequence_reconstruction/unrooted_tree.newick', 'abc', 'abc', '', False)
output_tree = raxml_seq_recon.root_tree('gubbins/tests/data/raxml_sequence_reconstruction/unrooted_tree.newick',raxml_seq_recon.temp_rooted_tree)
self.assertTrue(filecmp.cmp(str(raxml_seq_recon.temp_rooted_tree), 'gubbins/tests/data/raxml_sequence_reconstruction/expected_rooted_tree.newick', shallow = False))
def test_working_directory_construction(self):
raxml_seq_recon = RAxMLSequenceReconstruction('', '', '', '', '', False)
self.assertTrue( os.path.exists(raxml_seq_recon.working_dir) )
def test_ancestor_raxml_command_verbose(self):
raxml_seq_recon = RAxMLSequenceReconstruction('input_alignment.fasta', 'input_tree',
'output_alignment_filename', 'output_tree',
'raxmlHPC -f A -p 1 -m GTRGAMMA',
verbose = True)
self.assertEqual(raxml_seq_recon.raxml_reconstruction_command(raxml_seq_recon.working_dir+'/rooted_tree.newick'), 'raxmlHPC -f A -p 1 -m GTRGAMMA -s '+raxml_seq_recon.input_alignment_filename+' -t ' + raxml_seq_recon.working_dir+'/rooted_tree.newick -n internal ')
