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# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Helper script to update Codon tables from the NCBI.
These tables are based on parsing the NCBI file:
ftp://ftp.ncbi.nih.gov/entrez/misc/data/gc.prt
More detailed information about the tables are here:
https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi
This script is used to update Bio/Data/CodonTable.py
Note that the NCBI sometimes revise the older tables,
so don't just add new tables - replace all of them
and check for any differences in the old tables.
"""
import re
def line_wrap(text, indent=0, max_len=78, string=False):
"""Return a wrapped line if length is larger max_len.
The new parameter 'string' allows to wrap quoted text which is delimited
by single quotes. It adds a closing quote to the end of the line and an
opening quote to the start of the next line.
"""
split_len = max_len if not string else max_len - 2
if len(text) <= max_len:
return text
line = text[:split_len]
assert " " in line, line
line, rest = line.rsplit(" ", 1)
# New:
if string:
line += ' "'
rest = '"' + rest
rest = " " * indent + rest + text[split_len:]
assert len(line) < max_len
if indent + len(rest) <= max_len:
return line + "\n" + rest
else:
return line + "\n" + line_wrap(rest, indent, max_len, string)
print("##########################################################################")
print("# Start of auto-generated output from Scripts/update_ncbi_codon_table.py #")
print("##########################################################################")
print()
version = ""
for line in open("gc.prt").readlines():
if not version and line.startswith("-- Version"):
version = line.split("Version", 1)[1].strip()
print(f"# Data from NCBI genetic code table version {version}\n")
if line[:2] == " {":
names = []
id = None
aa = None
start = None
bases = []
elif line[:6] == " name":
names.append(re.search('"([^"]*)"', line).group(1))
elif line[:8] == " name":
names.append(re.search('"(.*)$', line).group(1))
elif line == ' Mitochondrial; Mycoplasma; Spiroplasma" ,\n':
names[-1] = names[-1] + " Mitochondrial; Mycoplasma; Spiroplasma"
elif line[:4] == " id":
id = int(re.search(r"(\d+)", line).group(1))
elif line[:10] == " ncbieaa ":
aa = line[12 : 12 + 64]
elif line[:10] == " sncbieaa":
start = line[12 : 12 + 64]
elif line[:9] == " -- Base":
bases.append(line[12 : 12 + 64])
elif line[:2] == " }":
assert names != [] and id is not None and aa is not None
assert start is not None and bases != []
if len(names) == 1:
names.append(None)
# Use %r instead of %s to include the quotes of the string!
print("register_ncbi_table(")
print(line_wrap(f' name="{names[0]}",', 4, string=True))
print(line_wrap(" alt_name=%s," % (repr(names[1]).replace("'", '"'))))
print(f" id={id:d},")
print(" table={")
s = " " * 8
noqa = False
for i in range(64):
if aa[i] != "*":
s += f'"{bases[0][i]}{bases[1][i]}{bases[2][i]}": "{aa[i]}", '
else:
# leave a space for stop codons
s += " " * 12
noqa = True
if i % 4 == 3:
# Print out in rows of four:
if noqa:
s += " # noqa: E241"
print(s.rstrip())
s = " " * 8
noqa = False
assert not s.strip()
print(" },")
codons = [
bases[0][i] + bases[1][i] + bases[2][i]
for i in range(64)
if start[i] == "*"
]
print(" stop_codons=%s," % repr(codons).replace("'", '"'))
codons = [
bases[0][i] + bases[1][i] + bases[2][i]
for i in range(64)
if start[i] == "M"
]
print(" start_codons=%s," % repr(codons).replace("'", '"'))
print(")")
print("")
elif line[:2] == "--" or line in ("\n", "}\n", "Genetic-code-table ::= {\n"):
pass
else:
raise Exception("Unparsed: " + repr(line))
print("########################################################################")
print("# End of auto-generated output from Scripts/update_ncbi_codon_table.py #")
print("########################################################################")
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