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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 used by Restriction to build the
Restriction_Dictionary.py module."""
from __future__ import print_function
import os
import sys
import time
import optparse
try:
from urllib import FancyURLopener
except ImportError:
#Python 3
from urllib.request import FancyURLopener
from Bio.Restriction.RanaConfig import *
class RebaseUpdate(FancyURLopener):
def __init__(self, e_mail='', ftpproxy=''):
"""RebaseUpdate([e_mail[, ftpproxy]]) -> new RebaseUpdate instance.
if e_mail and ftpproxy are not given RebaseUpdate uses the corresponding
variable from RanaConfig.
e_mail is the password for the anonymous ftp connection to Rebase.
ftpproxy is the proxy to use if any."""
proxy = {'ftp' : ftpproxy or ftp_proxy}
global Rebase_password
Rebase_password = e_mail or Rebase_password
if not Rebase_password:
raise FtpPasswordError('Rebase')
if not Rebase_name:
raise FtpNameError('Rebase')
FancyURLopener.__init__(self, proxy)
def prompt_user_passwd(self, host, realm):
return (Rebase_name, Rebase_password)
def openRebase(self, name = ftp_Rebase):
print('\n Please wait, trying to connect to Rebase\n')
try:
self.open(name)
except:
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)
self.retrieve(file, filename)
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 FtpPasswordError(ValueError):
def __init__(self, which_server):
print("\n\
\n In order to connect to %s ftp server, you must provide a password.\
\n Use the --e-mail switch to enter your e-mail address.\
\n\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('-m', '--e-mail',
action = "store",
dest = 'rebase_password',
default = '',
help = "set the e-mail address to be used as password for the"
"anonymous ftp connection to Rebase.")
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.rebase_password, option.ftp_proxy)
Getfiles.openRebase()
Getfiles.getfiles()
Getfiles.close()
sys.exit()
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