def validate_inputs(self):
"""Validate inputs."""
validate_bam_file(self.bam, check_exist=True)
validate_bed_file(self.output)
validate_string(self.quant, choices=["cDNA", "reads"])
validate_integer(self.multimax)
validate_string(self.group_by, choices=["start", "middle", "end"])
def validate_yes_no(self, column_name):
"""Validate that ``value`` is "yes" or "no"."""
for sample_name, element in zip(self.sample_names,
self.get_column(column_name)):
try:
validate_string(element,
choices=["yes", "no"],
allow_empty=True)
except ValueError:
self.error(
'SAMPLE: {} - Value {} in column {} should be "yes", "no" or empty.'
.format(sample_name, element, column_name))
def test_validate_string(self):
message = "Value 123 should be a string."
with self.assertRaisesRegex(ValueError, message):
validate_string(123)
message = "Value C should be one of A, B."
with self.assertRaisesRegex(ValueError, message):
validate_string("C", choices=["A", "B"])
validate_string("A")
validate_string("B", choices=["A", "B"])
validate_string("", allow_empty=True)