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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.
The Rebase EMBOSS files are used by `ranacompiler.py` to build the updated
`Restriction_Dictionary.py` module for `Bio.Restriction`.
"""
from __future__ import print_function
import os
import sys
import time
import optparse
try:
from urllib import FancyURLopener, urlcleanup
except ImportError:
# Python 3
from urllib.request import FancyURLopener, urlcleanup
from Bio.Restriction.RanaConfig import ftp_proxy, ftp_Rebase, Rebase_name
from Bio.Restriction.RanaConfig import ftp_emb_e, ftp_emb_s, ftp_emb_r
class RebaseUpdate(FancyURLopener):
def __init__(self, ftpproxy=''):
"""RebaseUpdate([ftpproxy]]) -> new RebaseUpdate instance.
if ftpproxy is not given RebaseUpdate uses the corresponding
variable from RanaConfig.
ftpproxy is the proxy to use if any.
"""
proxy = {'ftp': ftpproxy or ftp_proxy}
if not Rebase_name:
raise FtpNameError('Rebase')
if not proxy['ftp']:
proxy = {}
FancyURLopener.__init__(self, proxy)
def openRebase(self, name=ftp_Rebase):
print('\n Please wait, trying to connect to Rebase\n')
try:
self.open(name)
except Exception:
raise ConnectionError('Rebase')
return
def getfiles(self, *files):
for file in self.update(*files):
print('copying %s' % file)
fn = os.path.basename(file)
# filename = os.path.join(Rebase, fn)
filename = os.path.join(os.getcwd(), fn)
print('to %s' % filename)
try:
self.retrieve(file, filename)
# The following line is a workaround for an urllib bug in
# Python 2.7.11 - 2.7.xx (?). It does not seem to work on
# Python 3.xx. Try to remove the line in new Python versions.
urlcleanup()
except IOError as e:
print(e)
print('This error is probably due to a non-solved ftp bug in '
'recent Python versions. Please download the emboss '
'files manually from http://rebase.neb.com/rebase/'
'rebase.f37.html and then run ranacompiler.py. Find '
'more details in the Restriction manual.')
self.close()
return
self.close()
return
def localtime(self):
t = time.gmtime()
year = str(t.tm_year)[-1]
month = str(t.tm_mon)
if len(month) == 1:
month = '0' + month
return year + month
def update(self, *files):
if not files:
files = [ftp_emb_e, ftp_emb_s, ftp_emb_r]
return [x.replace('###', self.localtime()) for x in files]
def __del__(self):
if hasattr(self, 'tmpcache'):
self.close()
#
# self.tmpcache is created by URLopener.__init__ method.
#
return
class FtpNameError(ValueError):
def __init__(self, which_server):
print(" In order to connect to %s ftp server, you must provide a name.\
\n Please edit Bio.Restriction.RanaConfig\n" % which_server)
sys.exit()
class ConnectionError(IOError):
def __init__(self, which_server):
print('\
\n Unable to connect to the %s ftp server, make sure your computer\
\n is connected to the internet and that you have correctly configured\
\n the ftp proxy.\
\n Use the --proxy switch to enter the address of your proxy\
\n' % which_server)
sys.exit()
if __name__ == '__main__':
parser = optparse.OptionParser()
add = parser.add_option
add('-p', '--proxy',
action="store",
dest='ftp_proxy',
default='',
help="set the proxy to be used by the ftp connection.")
(option, args) = parser.parse_args()
Getfiles = RebaseUpdate(option.ftp_proxy)
Getfiles.openRebase()
Getfiles.getfiles()
Getfiles.close()
sys.exit()
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