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_get_annotations(conn):
"""Compare annotations from DB with expected annotations for each variant
Interrogation of `annotations` table.
"""
for index, variant in enumerate(VARIANTS):
read_tx = list(sql.get_annotations(conn, index + 1))[0]
del read_tx["variant_id"]
expected_tx = VARIANTS[index]["annotations"][0]
assert read_tx == expected_tx
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)