def pad(input, output, length, nterm):
"""Pad protein sequence to a specified length by adding amino acids in the
pattern of "GSGG".
INPUT and OUTPUT are paths to fasta files or "-" to specify STDIN/STDOUT.
"""
terminus = "N" if nterm else "C"
for (name, seq, qual) in readfq(input):
padded = pad_ggsg(seq, length, terminus)
pad_len = len(padded) - len(seq)
if pad_len > 0:
output_title = f"{name}|{terminus}-PADDED-{pad_len}"
else:
output_title = name
print(f">{output_title}\n{padded}", file=output)
def test_nonsense_terminus(self):
with raises(ValueError):
# note lowercase 'c'
padded = pad_ggsg(short_protein_seq,
len(short_protein_seq) + 5, "c")
def test_exact_len_seq(self):
padded = pad_ggsg(short_protein_seq, len(short_protein_seq), "C")
assert padded == short_protein_seq
def test_long_seq(self):
padded = pad_ggsg(short_protein_seq, len(short_protein_seq) - 3, "C")
assert padded == short_protein_seq
def test_c_term_pad(self):
padded = pad_ggsg(short_protein_seq, len(short_protein_seq) + 7, "C")
assert padded == short_protein_seq + "GGSGGGS"
def test_n_term_pad(self):
padded = pad_ggsg(short_protein_seq, len(short_protein_seq) + 5, "N")
assert padded == "GGSGG" + short_protein_seq