def test_main_position_zip(self):
fasta_filepath = "data/test.fasta.gz"
mask_filepath = "data/mask_position.txt"
mask_format = "position"
use_gzip = "true"
print_mask_ranges = "true"
output_fasta = "test.fasta.masked.gz"
applymask.main(mask_filepath, mask_format, fasta_filepath, use_gzip,
print_mask_ranges)
assert_fasta_zip(self, output_fasta, self.maskedsequence)
def test_main_unknown_mask(self):
fasta_filepath = "data/test.fasta.gz"
mask_filepath = "data/mask_range.tsv"
mask_format = "something"
use_gzip = "true"
print_mask_ranges = "true"
output_fasta = "test.fasta.masked.gz"
applymask.main(mask_filepath, mask_format, fasta_filepath, use_gzip,
print_mask_ranges)
assert_fasta_zip(self, output_fasta, self.maskedsequence)
def test_main_ranges_nozip(self):
fasta_filepath = "data/test.fasta"
mask_filepath = "data/mask_range.tsv"
mask_format = "range"
use_gzip = "false"
print_mask_ranges = "true"
output_fasta = "test.masked.fasta"
applymask.main(mask_filepath, mask_format, fasta_filepath, use_gzip,
print_mask_ranges)
assert_fasta(self, output_fasta, self.maskedsequence)