def test_mask_fasta_from_end(self, out_file, fasta_file, sequences):
mask.mask_fasta([], fasta_file, out_file, mask_from_end=3)
output = SeqIO.parse(out_file, "fasta")
for seq in output:
original = sequences[seq.id]
assert seq.seq[-3:] == "NNN"
assert seq.seq[:-3] == original.seq[:-3]
def test_mask_fasta_from_beginning_and_end_too_long(
self, fasta_file, out_file, beginning, end):
mask.mask_fasta([],
fasta_file,
out_file,
mask_from_beginning=beginning,
mask_from_end=end)
output = SeqIO.parse(out_file, "fasta")
for record in output:
assert record.seq == "N" * len(record.seq)
def test_mask_fasta_out_of_index(self, out_file, fasta_file, sequences):
"""mask_fasta provided a list of indexes past the length of the sequences"""
max_length = max(len(record.seq) for record in sequences.values())
mask.mask_fasta([5, max_length, max_length + 5], fasta_file, out_file)
output = SeqIO.parse(out_file, "fasta")
for seq in output:
assert seq[5] == "N", "Not all sites masked correctly!"
original = sequences[seq.id]
for idx, site in enumerate(seq):
if idx != 5:
assert site == original[idx], "Incorrect sites modified!"
def test_mask_fasta_invalid_sites(self, fasta_file, out_file, sequences,
mask_invalid):
"""Verify that mask_fasta masks invalid nucleotides when and only when mask_invalid is passed as True"""
mask.mask_fasta([], fasta_file, out_file, mask_invalid=mask_invalid)
output = SeqIO.to_dict(SeqIO.parse(out_file, "fasta"))
for name, record in sequences.items():
for site, nucleotide in enumerate(record.seq):
if nucleotide not in VALID_NUCLEOTIDES and mask_invalid is True:
assert output[name][site] == "N"
else:
assert output[name][site] == nucleotide
def test_mask_fasta_normal_case(self, fasta_file, out_file, sequences):
"""mask_fasta normal case - all sites in sequences"""
mask_sites = [5, 10]
mask.mask_fasta([5, 10], fasta_file, out_file)
output = SeqIO.parse(out_file, "fasta")
for seq in output:
original = sequences[seq.id]
for idx, site in enumerate(seq):
if idx not in mask_sites:
assert site == original[idx], "Incorrect sites modified!"
else:
assert site == "N", "Not all sites modified correctly!"