def test_binASC():
'''This test should pass'''
HERE = os.path.abspath(os.path.dirname(__file__))
full_path = os.path.join(HERE, "binASC")
main.call_main("morphology", '--no-ml-tree --min-subset-size 1 --raxml "%s"' % full_path)
def test_mixed():
'''This test should fail, as we've given PFinder a non-morph model'''
HERE = os.path.abspath(os.path.dirname(__file__))
full_path = os.path.join(HERE, "wrongmodel")
with pytest.raises(util.PartitionFinderError):
main.call_main("morphology", '--no-ml-tree --min-subset-size 1 --raxml "%s"' % full_path)
def test_clustering(folder_name):
full_path = os.path.join(HERE, folder_name)
error, kind, cmdline = test_container[folder_name]
if error is None:
main.call_main(kind, '"%s" --raxml %s' % (full_path, cmdline))
elif type(error) == type((0, 0)):
pytest.xfail(error[1])
else:
with pytest.raises(error):
main.call_main(kind, '"%s" --raxml %s' % (full_path, cmdline))
def test_model():
'''This test should pass'''
HERE = os.path.abspath(os.path.dirname(__file__))
full_path = os.path.join(HERE, "aictest")
main.call_main("morphology", '--no-ml-tree --min-subset-size 1 --raxml "%s"' % full_path)
new_file = os.path.join(full_path, "analysis/best_scheme.txt")
txt = open(new_file)
file_obj = txt.readlines()
for x in file_obj:
x = x.strip()
if "1 |" in x:
x = x.split('|')
mod = x[1].strip()
assert mod == 'MULTISTATE+G'
def test_bic():
'''This test should pass'''
HERE = os.path.abspath(os.path.dirname(__file__))
full_path = os.path.join(HERE, "bictest")
main.call_main("morphology", '--no-ml-tree --min-subset-size 1 --raxml "%s"' % full_path)
new_file = os.path.join(full_path, "analysis/best_scheme.txt")
txt = open(new_file)
file_obj = txt.readlines()
for x in file_obj:
x = x.strip()
if "Scheme BIC" in x:
line = x.split(':')
numspace = line[1]
num = numspace.strip()
num = float(num)
num = int(num)
assert num == 2
def test_model_greedy_phyml02(caplog):
with pytest.raises(util.PartitionFinderError):
main.call_main("DNA", '"%s"' % path_from_function())
assert "only works with nucleotide models" in caplog.text()
def test_model_greedy_raxml02(caplog):
with pytest.raises(util.PartitionFinderError):
main.call_main("DNA", '"%s" --raxml' % path_from_function())
assert "Expected ";" (at char 284), (line:9, col:22)" in caplog.text()
from partfinder import main, subset, scheme, config
from pympler.classtracker import ClassTracker
tracker = ClassTracker()
# Plug it in here..
scheme.tracker = tracker
scheme.tracker = tracker
tracker.track_class(subset.Subset)
tracker.track_class(scheme.Scheme)
tracker.create_snapshot()
main.call_main("DNA", "--raxml examples/nucleotide --cmd ' -T 2'")
# main.call_main("DNA", "--raxml Li_2008")
tracker.create_snapshot()
tracker.stats.print_summary()
def test_greedy_phyml_protein():
main.call_main("protein", '"%s"' % path_from_function())
def test_clustering_phyml_dna(caplog):
with pytest.raises(util.PartitionFinderError):
main.call_main("DNA", '--no-ml-tree "%s"' % path_from_function())
assert "Clustering methods are only available when using raxml" in caplog.text()
def test_quick_analysis(test_folder):
full_path = os.path.join(HERE, test_folder)
main.call_main("DNA", "%s --force-restart" % full_path)
def test_prot(prot):
full_path = os.path.join(HERE, prot)
main.call_main("protein", '--compare "%s"' % full_path)
def test_greedy_raxml_protein():
main.call_main("protein", '--no-ml-tree "%s" --raxml' % path_from_function())
def test_multi():
'''This test should pass'''
HERE = os.path.abspath(os.path.dirname(__file__))
full_path = os.path.join(HERE, "multistate")
main.call_main("morphology",
'--min-subset-size 1 --raxml "%s"' % full_path)
def test_dna(dna):
full_path = os.path.join(HERE, dna)
main.call_main("DNA", '--compare "%s"' % full_path)
def test_model_greedy_raxml02(caplog):
with pytest.raises(util.PartitionFinderError):
main.call_main("DNA", '"%s" --raxml' % path_from_function())
assert "Expected "
" (at char 284), (line:9, col:22)" in caplog.text()
def test_model_greedy_raxml01(caplog):
with pytest.raises(util.PartitionFinderError):
main.call_main("DNA", '"%s" --raxml' % path_from_function())
assert "WAG+F' is not a valid model for phylogeny program raxml" in caplog.text(
)
def test_model_greedy_phyml02(caplog):
with pytest.raises(util.PartitionFinderError):
main.call_main("DNA", '"%s"' % path_from_function())
assert "only works with nucleotide models" in caplog.text()
def test_overlap_error(caplog):
with pytest.raises(util.PartitionFinderError):
main.call_main("protein", '"%s"' % path_from_function())
assert "overlaps with previously defined partitions" in caplog.text()
def test_rerun_success(rerun_success):
full_path = os.path.join(HERE, rerun_success)
load_rerun(full_path)
main.call_main("DNA", '"%s"' % full_path)
def test_1subset():
full_path = os.path.join(HERE, "1subset")
main.call_main("DNA", '--raxml "%s"' % full_path)
def test_rerun_pf_error(rerun_pf_error):
full_path = os.path.join(HERE, rerun_pf_error)
load_rerun(full_path)
with pytest.raises(util.PartitionFinderError):
main.call_main("DNA", '"%s"' % full_path)
def test_alignment_error(caplog):
with pytest.raises(alignment.AlignmentError):
main.call_main("protein", '--no-ml-tree "%s"' % path_from_function())
assert "Site 1000 is specified in [data_blocks], but the alignment only has 949 sites." in caplog.text()
def test_rerun_analysis_error(rerun_ana_error):
full_path = os.path.join(HERE, rerun_ana_error)
load_rerun(full_path)
with pytest.raises(analysis.AnalysisError):
main.call_main("DNA", '"%s"' % full_path)
def test_morph_tiger():
full_path = os.path.join(HERE, "morph_tiger")
main.call_main("morphology", '--raxml --kmeans tiger --min-subset-size 1 "%s"' % full_path)
def test_rerun_config_error(rerun_conf_error):
full_path = os.path.join(HERE, rerun_conf_error)
load_rerun(full_path)
with pytest.raises(config.ConfigurationError):
main.call_main("DNA", '"%s"' % full_path)
def test_overlapping_blocks(caplog):
with pytest.raises(PartitionFinderError):
main.call_main("protein", '--no-ml-tree "%s"' % path_from_function())
assert "following sites overlap" in caplog.text()
def test_clustering_raxml_dna():
main.call_main("DNA", '--no-ml-tree "%s" --raxml' % path_from_function())
def test_greedy_raxml_dna():
main.call_main("DNA", '"%s" --raxml' % path_from_function())
def test_alignment_error(caplog):
with pytest.raises(alignment.AlignmentError):
main.call_main("protein", '--no-ml-tree "%s"' % path_from_function())
assert "Site 1000 is specified in [data_blocks], but the alignment only has 949 sites." in caplog.text(
)
def test_overlap_error(caplog):
with pytest.raises(util.PartitionFinderError):
main.call_main("protein", '"%s"' % path_from_function())
assert "overlaps with previously defined partitions" in caplog.text()
def test_overlapping_blocks(caplog):
with pytest.raises(PartitionFinderError):
main.call_main("protein", '--no-ml-tree "%s"' % path_from_function())
assert "following sites overlap" in caplog.text()
def test_model_greedy_phyml03(caplog):
with pytest.raises(util.PartitionFinderError):
main.call_main("DNA", '"%s"' % path_from_function())
assert "'WAG+LG+F+I' is not a valid model for phylogeny program phyml" in caplog.text()
def test_missing_sites_warning(caplog):
main.call_main("protein", '--no-ml-tree "%s"' % path_from_function())
assert "These columns are missing from the block definitions" in caplog.text(
)
def test_model_greedy_raxml03(caplog):
with pytest.raises(util.PartitionFinderError):
main.call_main("DNA", '"%s" --raxml' % path_from_function())
assert "MtArt+I+G+F' is not a valid model for phylogeny program raxml" in caplog.text()
def test_bin():
'''This test should pass'''
HERE = os.path.abspath(os.path.dirname(__file__))
full_path = os.path.join(HERE, "bin_wrongdata")
main.call_main("morphology",
'--no-ml-tree --min-subset-size 1 --raxml "%s"' % full_path)
def test_overlap_error(caplog):
with pytest.raises(util.PartitionFinderError):
main.call_main("protein", '--no-ml-tree "%s"' % path_from_function())
assert "sites overlap in your block definitions" in caplog.text()
def test_grand():
full_path = os.path.join(HERE, "Grande_2013")
main.call_main("DNA", '--no-ml-tree --raxml "%s"' % full_path)
def test_clustering_phyml_dna(caplog):
with pytest.raises(util.PartitionFinderError):
main.call_main("DNA", '--no-ml-tree "%s"' % path_from_function())
assert "Clustering methods are only available when using raxml" in caplog.text(
)
def test_incmat():
'''This test should fail due to incorrect line length'''
HERE = os.path.abspath(os.path.dirname(__file__))
full_path = os.path.join(HERE, "incmat")
with pytest.raises(util.PartitionFinderError):
main.call_main("morphology", '--no-ml-tree --min-subset-size 1 --raxml "%s"' % full_path)
def test_grand():
full_path = os.path.join(HERE, "Grande_2013")
main.call_main("DNA", '--raxml "%s"' % full_path)
def test_greedy_phyml_dna():
main.call_main("DNA", '"%s"' % path_from_function())
def test_greedy_phyml_dna():
main.call_main("DNA", '--no-ml-tree "%s"' % path_from_function())
def test_greedy_raxml_dna():
main.call_main("DNA", '"%s" --raxml' % path_from_function())
def test_clustering_raxml_dna():
main.call_main("DNA", '--no-ml-tree "%s" --raxml' % path_from_function())
def test_greedy_phyml_protein():
main.call_main("protein", '"%s"' % path_from_function())
def test_overlap_error(caplog):
with pytest.raises(util.PartitionFinderError):
main.call_main("protein", '--no-ml-tree "%s"' % path_from_function())
assert "sites overlap in your block definitions" in caplog.text()
def test_greedy_raxml_protein():
main.call_main("protein", '"%s" --raxml' % path_from_function())
def test_morph_entropy():
full_path = os.path.join(HERE, "morph_entropy")
main.call_main("morphology", '--raxml --kmeans entropy --min-subset-size 1 "%s"' % full_path)
def test_model_greedy_phyml03(caplog):
with pytest.raises(util.PartitionFinderError):
main.call_main("DNA", '"%s"' % path_from_function())
assert "'WAG+LG+F+I' is not a model/list that is implemented in PartitionFinder." in caplog.text()
def test_DNA_entropy():
full_path = os.path.join(HERE, "DNA_entropy")
with pytest.raises(util.PartitionFinderError):
main.call_main("DNA", '--raxml --kmeans entropy --min-subset-size 10 "%s"' % full_path)
def test_model_greedy_raxml03(caplog):
with pytest.raises(util.PartitionFinderError):
main.call_main("DNA", '"%s" --raxml' % path_from_function())
assert "'MTART+I+G+F, WAG+I+G' is/are not a valid model(s)" in caplog.text()
def test_missing_sites_warning(caplog):
main.call_main("protein", '--no-ml-tree "%s"' % path_from_function())
assert "These columns are missing from the block definitions" in caplog.text()
def test_grand():
full_path = os.path.join(HERE, "Grande_2013")
with pytest.raises(util.PartitionFinderError):
main.call_main("DNA", '--no-ml-tree --raxml "%s"' % full_path)
def test_quick_analysis(test_folder):
full_path = os.path.join(HERE, test_folder)
main.call_main("DNA", '--no-ml-tree "%s" --force-restart' % full_path)
def test_quick_analysis(test_folder):
full_path = os.path.join(HERE, test_folder)
main.call_main("DNA", '"%s" --force-restart' % full_path)