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import io
def nucleotide_complements_table():
# A nice list of complements can be found at:
# http://www.reverse-complement.com/ambiguity.html
complements = dict(
A="T",
C="G",
G="C",
T="A",
a="t",
c="g",
g="c",
t="a",
U="A",
u="a",
# R, purine (A, G) vs Y, pyrimidine (C, T)
R="Y",
Y="R",
r="y",
y="r",
# K, keto (G, T) vs A, amino (A, C)
K="M",
M="K",
k="m",
m="k",
# B, not A, vs V, not T
B="V",
V="B",
b="v",
v="b",
# D, not C vs H, not G
D="H",
H="D",
d="h",
h="d",
# S, W and N's complements are the same. So they are not explicitly
# included above
)
table = []
for i in range(256):
c = chr(i)
if c in complements:
table.append(f"'{complements[c]}'")
else:
table.append(i)
return table
def make_table(variable_name, table, columns=16):
out = io.StringIO()
out.write(variable_name + " = {")
for i, literal in enumerate(table):
if i % columns == 0:
out.write("\n ")
out.write(f"{literal:3}, ")
out.write("\n")
out.write("};\n")
return out.getvalue()
def main():
with open("src/dnaio/_conversions.h", "wt", encoding="utf-8") as out:
out.write(
"// This file is generated by generate_conversion_tables.py\n"
"// Please do not edit manually.\n\n"
)
out.write(
make_table(
"static const char NUCLEOTIDE_COMPLEMENTS[256]",
nucleotide_complements_table(),
)
)
if __name__ == "__main__":
main()
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