def testIsValidWithMetadata(self):
# Create one valid DSV file
content = """@title: test
#CHROM.POS.ID.REF.ALT.QUAL.FILTER
20.14370.rs6054257.G.A.29.PASS
20.17330. ..A.3.q10 low
20.1110696.rs6040355.A.G,T.67.PASS
.1230237..T..47.
20.1234567.microsat1.GTC.G,GTCT.50.
......"""
with open(self.tmp_out_dsv, "w") as FH_out:
FH_out.write(content)
# Check isValid
self.assertTrue(not SVIO.isValid(self.tmp_out_dsv, ".", "@"))
# Create one valid DSV file
content = """@title: test
#CHROM.POS.ID.REF.ALT.QUAL.FILTER
20.14370.rs6054257.G.A.29.PASS
20.17330. ..A.3.q10 low
20.1110696.rs6040355.A.G,T.67.PASS
.1230237..T..47.
20.1234567.microsat1.GTC.G,GTCT.50.
......"""
with open(self.tmp_out_dsv, "w") as FH_out:
FH_out.write(content)
# Check isValid
self.assertTrue(SVIO.isValid(self.tmp_out_dsv, ".", "@"))
# Check if file pointer is ok in reopen
observed_rows = []
with open(self.tmp_out_dsv) as FH_in:
for row_idx, readed_row in enumerate(FH_in):
observed_rows.append(readed_row)
self.assertEqual(content, "".join(observed_rows))
def testIsValidTrue(self):
# Create one valid DSV file
rows = deepcopy(self.data["rows"])
rows.insert(0, self.data["titles"])
rows.extend([
["1", "1234567", "microsat1", "GTC", "G,GTCT", "50", ""],
["1", "1234567", "microsat1", "GTC", "G,GTCT", "50", ""],
["1", "1234567", "microsat1", "GTC", "G,GTCT", "50", ""],
["1", "1234567", "microsat1", "GTC", "G,GTCT", "50", ""],
["1", "1234567", "microsat1", "GTC", "G,GTCT", "50", ""],
["1", "1234567", "microsat1", "GTC", "G,GTCT", "50", ""],
["1", "1234567", "microsat1", "GTC", "G,GTCT", "50", ""],
["1", "1234567", "microsat1", "GTC", "G,GTCT", "50", ""]
])
with open(self.tmp_out_dsv, "w") as FH_out:
for curr_row in rows:
FH_out.write(".".join(curr_row) + "\n")
# Check isValid
self.assertEqual(True, SVIO.isValid(self.tmp_out_dsv, "."))
# Check if fie pointer is ok in reopen
with open(self.tmp_out_dsv) as FH_in:
for row_idx, readed_row in enumerate(FH_in):
expected_row = ".".join(rows[row_idx]) + "\n"
self.assertEqual(expected_row, readed_row)