def conn():
# Do not use ":memory:" ! SqlThread open the file
tempdb = tempfile.mkstemp(suffix=".db")[1]
conn = sql.get_sql_connection(tempdb)
importer.import_reader(
conn, VcfReader(open("examples/test.snpeff.vcf"), "snpeff"))
return conn
def test_import_pedfile():
"""Test import of samples from .tfam PED file"""
reader = VcfReader(open("examples/test.snpeff.vcf"), "snpeff")
conn = sqlite3.connect(":memory:")
import_reader(conn, reader)
import_pedfile(conn, "examples/test.snpeff.pedigree.tfam")
samples = [dict(row) for row in conn.execute("SELECT * FROM samples")]
print("Found samples:", samples)
expected_first_sample = {
"id": 1,
"name": "NORMAL",
"family_id": "fam",
"father_id": 2,
"mother_id": 1,
"sex": 2,
"phenotype": 1,
}
expected_second_sample = {
"id": 2,
"name": "TUMOR",
"family_id": "fam",
"father_id": 0,
"mother_id": 0,
"sex": 1,
"phenotype": 2,
}
# Third sample is not conform
assert len(samples) == 2
assert expected_first_sample in samples
assert expected_second_sample in samples
def conn():
# Required a real file to make it work !
tempdb = tempfile.mkstemp(suffix=".db")[1]
conn = sql.get_sql_connection(tempdb)
importer.import_reader(
conn, VcfReader(open("examples/test.snpeff.vcf"), "snpeff"))
return conn
def conn():
conn = sql.get_sql_connection(":memory:")
import_reader(conn, VcfReader(open("examples/test.snpeff.vcf"), "snpeff"))
return conn
def on_fields_changed(self):
if self.mainwindow is None or self._is_refreshing:
return
self.mainwindow.state.fields = self.model.fields
self.mainwindow.refresh_plugins(sender=self)
if __name__ == "__main__":
import sys
from cutevariant.core.importer import import_reader
from cutevariant.core.reader import FakeReader
app = QApplication(sys.argv)
conn = sql.get_sql_connection(":memory:")
import_reader(conn, FakeReader())
# import_file(conn, "examples/test.snpeff.vcf")
view = FieldsEditorWidget()
view.conn = conn
view.fields = ["chr", "pos"]
# view.changed.connect(lambda : print(view.columns))
view.show()
app.exec_()
def test_import(reader):
conn = sqlite3.connect(":memory:")
import_reader(conn, reader)