def test_advanced_get_one_variant(conn):
"""Test getting variant from variant_id
.. note:: annotations and samples which are optional ARE tested here
"""
for variant_id, expected_variant in enumerate(VARIANTS, 1):
found_variant = sql.get_one_variant(conn,
variant_id,
with_annotations=True,
with_samples=True)
for extra_field in ("annotations", "samples"):
assert isinstance(found_variant[extra_field],
list), "Type not expected"
for item in found_variant[extra_field]:
# Remove variant_id and sample_id from sample/annotation before test
if "variant_id" in item:
del item["variant_id"]
if "sample_id" in item:
del item["sample_id"]
if extra_field in found_variant and extra_field in expected_variant:
assert found_variant[extra_field] == expected_variant[
extra_field]
def populate(self):
"""Show the current variant attributes on the TreeWidget
.. note:: RichText in Markdown is supported starting PySide 5.14
"""
if not self.current_variant or "id" not in self.current_variant:
return
variant_id = self.current_variant["id"]
# Populate variant
data = dict(
[
(k, v)
for k, v in sql.get_one_variant(self.conn, variant_id).items()
if k not in ("variant_id", "sample_id", "annotations", "samples")
]
)
self.variant_view.set_dict(data)
self.edit_panel.set_data(data)
title = "{chr}:{pos} {ref}>{alt}".format(**data)
# self.parent().setWindowTitle(title)
# Populate annotations
self.transcript_combo.blockSignals(True)
self.transcript_combo.clear()
for annotation in sql.get_annotations(self.conn, variant_id):
if "transcript" in annotation:
self.transcript_combo.addItem(annotation["transcript"], annotation)
self.on_transcript_changed()
self.transcript_combo.blockSignals(False)
# Populate samples
self.sample_combo.blockSignals(True)
self.sample_combo.clear()
for sample in sql.get_samples(self.conn):
self.sample_combo.addItem(sample["name"], sample["id"])
self.on_sample_changed()
self.sample_combo.blockSignals(False)
# Populate genotypes for samples
self.genotype_view.clear()
query = f"""SELECT samples.name, sv.gt FROM samples
LEFT JOIN sample_has_variant sv ON samples.id = sv.sample_id
AND sv.variant_id = {variant_id}"""
for sample_name, genotype in self.conn.execute(query):
item = QListWidgetItem()
icon = self.genotype_icons.get(genotype, self.genotype_icons[-1])
item.setText(sample_name)
item.setIcon(icon)
item.setToolTip(cm.GENOTYPE_DESC.get(genotype, -1))
self.genotype_view.addItem(item)
def test_update_variant(conn):
"""Test update procedure of a variant in DB (modify some of its field values)
.. note:: exception si pas id, ajout comment
"""
# Update the first variant data
updated = {"id": 1, "ref": "A", "chr": "chrX"}
sql.update_variant(conn, updated)
inserted = sql.get_one_variant(conn, 1)
assert inserted["ref"] == updated["ref"]
assert inserted["chr"] == updated["chr"]
def test_get_one_variant(conn):
"""Test getting variant from variant_id
.. note:: annotations and samples which are optional are not tested here
=> see :meth:`test_advanced_get_one_variant`
"""
for variant_id, expected_variant in enumerate(VARIANTS, 1):
found_variant = sql.get_one_variant(conn, variant_id)
print("found variant", found_variant)
assert found_variant["id"] == variant_id
for k, v in expected_variant.items():
if k not in ("annotations", "samples"):
assert found_variant[k] == expected_variant[k]
def populate(self):
"""Show the current variant attributes on the TreeWidget
.. note:: RichText in Markdown is supported starting PySide 5.14
"""
if not self.current_variant or "id" not in self.current_variant:
return
variant_id = self.current_variant["id"]
# Populate variant
self.populate_tree_widget(self.variant_view,
sql.get_one_variant(self.conn, variant_id))
# Populate annotations
self.transcript_combo.blockSignals(True)
self.transcript_combo.clear()
for annotation in sql.get_annotations(self.conn, variant_id):
if "transcript" in annotation:
self.transcript_combo.addItem(annotation["transcript"],
annotation)
self.on_transcript_changed()
self.transcript_combo.blockSignals(False)
# Populate samples
self.sample_combo.blockSignals(True)
self.sample_combo.clear()
for sample in sql.get_samples(self.conn):
self.sample_combo.addItem(sample["name"], sample["id"])
self.on_sample_changed()
self.sample_combo.blockSignals(False)
# Populate genotypes for samples
self.genotype_view.clear()
query = f"""SELECT samples.name, sv.gt FROM samples
LEFT JOIN sample_has_variant sv ON samples.id = sv.sample_id
AND sv.variant_id = {variant_id}"""
for sample_name, genotype in self.conn.execute(query):
item = QListWidgetItem()
icon = self.genotype_icons.get(genotype, self.genotype_icons[-1])
item.setText(sample_name)
item.setIcon(icon)
item.setToolTip(cm.GENOTYPE_DESC.get(genotype, -1))
self.genotype_view.addItem(item)
# if "variant_view" in self.mainwindow.plugins:
# main_view = self.mainwindow.plugins["variant_view"]
# print(main_view)
# sql.update_variant(self.conn, updated)
# def show_menu(self, pos: QPoint):
# """Show context menu associated to the current variant"""
# if not self.current_variant:
# return
# self.context_menu.popup(self.current_variant, self.view.mapToGlobal(pos))
if __name__ == "__main__":
import sys
app = QApplication(sys.argv)
conn = get_sql_connection("/home/schutz/Dev/cutevariant/examples/test.db")
w = VariantInfoWidget()
w.conn = conn
variant = sql.get_one_variant(conn, 1)
w.current_variant = variant
w.show()
app.exec_()
