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#!/usr/bin/env python
#
# Restriction Analysis Libraries.
# Copyright (C) 2004. Frederic Sohm.
#
# 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.
#
"""Update the Rebase EMBOSS files and NCBI LinkOut files.
These two sets of files are used by ``ranacompiler.py`` to build the updated
``Restriction_Dictionary.py`` module for ``Bio.Restriction``.
"""
import os
from datetime import date
from urllib.request import urlcleanup
from urllib.request import urlretrieve
# Rebase ftp location, do not modify these addresses:
ftp_Rebase = "ftp://ftp.neb.com/"
ftp_emb_e = ftp_Rebase + "pub/rebase/emboss_e.###"
ftp_emb_s = ftp_Rebase + "pub/rebase/emboss_s.###"
ftp_emb_r = ftp_Rebase + "pub/rebase/emboss_r.###"
ftp_bairoch = ftp_Rebase + "pub/rebase/bairoch.###"
# Generate 'time stamp' of type ymm to add to Rebase file names.
# This is the 3 digit number REBASE release number (e.g. 312).
# The first digit is the last digit of the year (e.g. 3 for 2013)
# and the two last the month (e.g. 12 for December)
release_number = date.today().strftime("%y%m")[1:]
# Replace '###' with the 'time stamp'
files = [
x.replace("###", release_number)
for x in [ftp_emb_e, ftp_emb_s, ftp_emb_r, ftp_bairoch]
]
def get_files():
"""Download Rebase and LinkOut files."""
print(f"Preparing to download {len(files)} files")
for file in files:
print(f"copying {file}")
fn = os.path.basename(file)
filename = os.path.join(os.getcwd(), fn)
print(f"to {filename}")
try:
urlretrieve(file, filename)
urlcleanup()
except OSError as e:
print(e)
print(
"Download of Rebase files failed. Please download the files "
f'"emboss_e.{release_number}", "emboss_s.{release_number}", "emboss_r.{release_number}", and "bairoch.{release_number}" manually '
"from: ftp://ftp.neb.com/pub/rebase."
)
return
if __name__ == "__main__":
get_files()
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