def view_test_results(name: Optional[str] = None):
"""
View the results of a particular test.
:param name: Name, or `None` to use the currently loaded model.
"""
if name:
tdir = TestDirectory(name)
groot.file_load(tdir.r_model)
model = groot.current_model()
groot.print_trees(model.user_graphs["original_graph"],
format=groot.EFormat._HTML,
file="open")
groot.print_trees(model.fusion_graph_unclean,
format=groot.EFormat._HTML,
file="open")
groot.print_trees(model.fusion_graph_clean,
format=groot.EFormat._HTML,
file="open")
for component in model.components:
groot.print_trees(component.named_tree_unrooted,
format=groot.EFormat._HTML,
file="open")
groot.print_trees(component.named_tree,
format=groot.EFormat._HTML,
file="open")
report = model.user_reports["test_differences"].html
with OpeningWriter() as view_report:
view_report.write(report)
def _refresh_labels( self ):
# Wizard
wt = groot.Wizard.get_active()
if wt is not None and wt.is_paused:
self.ui.FRA_PAUSED.setVisible( True )
self.ui.LBL_NEXT.setText( wt.get_stage_name() )
else:
self.ui.FRA_PAUSED.setVisible( False )
# Others
m = groot.current_model()
for stage, indicator, label, box, btn in self.map:
status = m.get_status( stage )
if status.is_hot:
indicator.setStyleSheet( "background:red;" + self.INDICATOR_SUFFIX )
elif status.is_complete:
indicator.setStyleSheet( "background:green;" + self.INDICATOR_SUFFIX )
elif status.is_partial:
indicator.setStyleSheet( "background:orange;" + self.INDICATOR_SUFFIX )
else:
indicator.setStyleSheet( "background:silver;" + self.INDICATOR_SUFFIX )
box.setText( str( status ) )
def on_BTN_SEQUENCE_clicked(self) -> None:
"""
Signal handler:
"""
accession = self.seq_view.get_gene_name(self.seq_view.highlight_row)
if accession:
gene: groot.Gene = groot.current_model().genes[accession]
self.inspect_elsewhere(gene)
def on_BTN_POSITION_clicked(self) -> None:
"""
Signal handler:
"""
accession = self.seq_view.get_gene_name(self.seq_view.highlight_row)
if accession:
gene: groot.Gene = groot.current_model().genes[accession]
col = self.seq_view.highlight_col
domains = list(x for x in gene.iter_userdomains()
if x.start <= col <= x.end)
self.inspect_elsewhere(domains)
def on_BTN_SITE_clicked(self) -> None:
"""
Signal handler:
"""
accession = self.seq_view.get_gene_name(self.seq_view.highlight_row)
if accession:
gene: groot.Gene = groot.current_model().genes[accession]
col = self.seq_view.highlight_col
site = self.seq_view.get_site_text(self.seq_view.highlight_row,
col)
domains = list(
x for x in gene.iter_userdomains()
if x.start <= col <= x.end and x.site_array[col] == site)
self.inspect_elsewhere(domains)
def run_test(name: str) -> groot.EChanges:
"""
Runs a test case and saves the results to the global results folder.
:param name: A name or path to the test case.
If no full path is provided the "samples" folder will be assumed.
The test case folder must contain:
* The data (BLAST, FASTA)
* A `tree.csv` file describing the expected results (in edge-list format)
* A `groot.ini` file describing the parameters to use.
:return: Nothing is returned, the results are saved to the global results folder.
"""
# Load sample file
tdir = TestDirectory(name)
# Define outputs
file_helper.create_directory(tdir.r_folder, overwrite=True)
# Check the requisite files exist
if not os.path.isdir(tdir.t_folder):
raise ValueError(
"This is not a test case (it is not even a folder, «{}»).".format(
tdir.t_folder))
if not os.path.isfile(tdir.t_tree):
raise ValueError(
"This is not a test case (it is missing the edge list file, «{}»)."
.format(tdir.t_tree))
if not os.path.isfile(tdir.t_ini):
raise ValueError(
"This is not a test case (it is missing the INI file, «{}»).".
format(tdir.t_ini))
# Read the test specs
specs = io_helper.load_ini(tdir.t_ini)
if "groot_test" not in specs:
raise ValueError(
"This is not a test case (it is missing the `groot_test` section from the INI file, «{}»)."
.format(tdir.t_ini))
if not "groot_wizard" in specs:
raise ValueError(
"This is not a test case (it is missing the «wizard» section from the INI «{}»)."
.format(tdir.t_ini))
wizard_params = specs["groot_wizard"]
try:
wiz_tol = int(wizard_params["tolerance"])
wiz_og = wizard_params["outgroups"].split(",")
except KeyError as ex:
raise ValueError(
"This is not a test case (it is missing the «{}» setting from the «wizard» section of the INI «{}»)."
.format(ex, tdir.t_ini))
# Copy the test files to the output folder
for file in file_helper.list_dir(tdir.t_folder):
shutil.copy(
file, file_helper.format_path(file,
tdir.r_folder + "/input_{N}{E}"))
# Create settings
walkthrough = groot.Wizard(
new=True,
name=tdir.r_model,
imports=groot.sample_data.get_sample_contents(tdir.t_folder),
pauses=set(),
tolerance=wiz_tol,
outgroups=wiz_og,
alignment="",
tree="maximum_likelihood", # "neighbor_joining",
view=False,
save=False,
supertree="clann")
try:
# Execute the wizard (no pauses are set so this only requires 1 `step`)
walkthrough.make_active()
walkthrough.step()
if not walkthrough.is_completed:
raise ValueError("Expected wizard to complete but it did not.")
# Add the original graph to the Groot `Model` in case we debug
test_tree_file_data = groot.UserGraph(mgraph.importing.import_edgelist(
file_helper.read_all_text(tdir.t_tree), delimiter="\t"),
name="original_graph")
groot.rectify_nodes(test_tree_file_data.graph, groot.current_model())
groot.current_model().user_graphs.append(
groot.FixedUserGraph(test_tree_file_data.graph, "original_graph"))
finally:
# Save the final model regardless of whether the test succeeded
groot.file_save(tdir.r_model)
# Perform the comparison
model = groot.current_model()
differences = groot.compare_graphs(model.fusion_graph_clean,
test_tree_file_data)
q = differences.raw_data["quartets"]["match_quartets"]
print("match_quartets: " + q)
# Write the results---
# ---Summary
io_helper.save_ini(tdir.r_summary, differences.raw_data)
# ---Alignments
groot.print_alignments(file=tdir.r_alignments)
# ---Differences
file_helper.write_all_text(tdir.r_comparison,
differences.html,
newline=True)
differences.name = "test_differences"
groot.current_model().user_reports.append(differences)
# ---Model
groot.file_save(tdir.r_model)
# Done
intermake.pr.printx(
"<verbose>The test has completed, see «{}».</verbose>".format(
tdir.r_comparison))
return groot.EChanges.MODEL_OBJECT
def get_model(self) -> groot.Model:
return groot.current_model()
def __init__(self, parent):
super().__init__(parent)
self.setWindowTitle("Genes")
self.queue = []
root_layout = qt.QVBoxLayout()
self.setLayout(root_layout)
toolbar = qt.QFrame()
root_layout.addWidget(toolbar)
self.tool_layout = qt.QHBoxLayout()
self.tool_layout.setContentsMargins(qt.QMargins(0, 0, 0, 0))
toolbar.setLayout(self.tool_layout)
self.add_select_button(toolbar)
self.add_toolbar_item("Import\nnames", resources.rename.icon(),
self.on_mnu_rename)
qt.toolbar_helper.add_spacer(toolbar)
self.add_toolbar_item("Refresh", resources.refresh.icon(),
self.refresh_data)
self.add_toolbar_item("Help", resources.help.icon(), self.on_mnu_help)
self.scroll_area = qt.QScrollArea()
self.scroll_area.setWidgetResizable(True)
self.scroll_area.setSizePolicy(qt.QSizePolicy.MinimumExpanding,
qt.QSizePolicy.Expanding)
self.scroll_area.setHorizontalScrollBarPolicy(qt.Qt.ScrollBarAlwaysOff)
self.scroll_area.setMinimumWidth(1024)
root_layout.addWidget(self.scroll_area)
frame = qt.QWidget()
self.scroll_area.setWidget(frame)
self.layout = qt.QGridLayout()
self.layout.setContentsMargins(qt.QMargins(0, 0, 0, 0))
frame.setLayout(self.layout)
self.model = groot.current_model()
self.setStyleSheet("""
QAbstractButton[style="custom"]
{
background: white;
border: 2px solid white;
border-radius: 4px;
}
QAbstractButton[style="custom"]:hover
{
border: 2px solid black;
}
QAbstractButton[style="custom"]:pressed
{
border: 2px solid silver;
}
QAbstractButton[style="custom"]:checked
{
background: #03A9F4;
}
""")
self.lut: Dict[groot.Gene,
Tuple[qt.QLineEdit, qt.QAbstractButton,
qt.QAbstractButton, qt.QAbstractButton]] = {}
self.refresh_data()
btn_box = qt.QDialogButtonBox()
btn_box.setStandardButtons(qt.QDialogButtonBox.Apply
| qt.QDialogButtonBox.Ok
| qt.QDialogButtonBox.Cancel)
btn_box.button(qt.QDialogButtonBox.Apply).clicked.connect(
self.on_apply)
btn_box.button(qt.QDialogButtonBox.Ok).clicked.connect(self.on_ok)
btn_box.button(qt.QDialogButtonBox.Cancel).clicked.connect(
self.on_cancel)
root_layout.addWidget(btn_box)
def _on_gene(self, name: str):
if name == "none":
return
gene = groot.current_model().genes[name]
self.inspect_elsewhere(gene)