Package Bio :: Package Restriction :: Module RanaConfig
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Source Code for Module Bio.Restriction.RanaConfig

 1  # 
 2  #      Restriction Analysis Libraries. 
 3  #      Copyright (C) 2004. Frederic Sohm. 
 4  # 
 5  # This code is part of the Biopython distribution and governed by its 
 6  # license.  Please see the LICENSE file that should have been included 
 7  # as part of this package. 
 8  # 
 9   
10  import os 
11   
12  ############################################################################### 
13  #                   Configuration of the console. 
14  # 
15  #   Mainly used  by PrintFormat.PrintFormat 
16  # 
17  #   ConsoleWidth : width of the console used default to 80. 
18  #                   should never be less than 60. 
19  #   NameWidth    : space attributed to the name in PrintList method. 
20  #   Indent       : Indent of the second line. 
21  #   MaxSize      : Maximal size of the sequence (default=6: 
22  #                                                -> 99 999 bp + 1 trailing ',' 
23  #                  people are unlikely to ask for restriction map of sequences 
24  #                  bigger than 100.000 bp. This is needed to determine the 
25  #                  space to be reserved for sites location. 
26  #                    
27  #                  MaxSize = 5  =>   9.999 bp 
28  #                  MaxSize = 6  =>  99.999 bp 
29  #                  MaxSize = 7  => 999.999 bp 
30  #   example: 
31  #                
32  #   <------------ ConsoleWidth ---------------> 
33  #   <- NameWidth -> 
34  #   EcoRI         :   1, 45, 50, 300, 400, 650, 
35  #                         700, 1200, 2500. 
36  #                     <--> 
37  #                       Indent 
38  # 
39  ConsoleWidth        =     80                    
40  NameWidth           =     10 
41  Indent              =     4 
42  MaxSize             =     6  
43  ############################################################################### 
44  #                   Proxies 
45  # 
46  #   Enter here the address of your proxy if any. 
47  #   If you don't use proxy use an empty string 
48  #   i.e. 
49  #   ftp_proxy       =   '' 
50  #                   -> no proxy 
51  # 
52  #   ftp_proxy       =   'http://www.somewhere.something:one_number' 
53  #                   -> www.somewhere.something is the address of the proxy. 
54  #                      one_number is the port number. 
55  #    
56  ftp_proxy           =   '' 
57  ############################################################################### 
58  #                   Rebase ftp location 
59  # 
60  #   Do not modify the addresses. 
61  # 
62  ftp_Rebase          =   'ftp://ftp.neb.com/' 
63  ftp_emb_e           =   ftp_Rebase+'pub/rebase/emboss_e.###' 
64  ftp_emb_s           =   ftp_Rebase+'pub/rebase/emboss_s.###' 
65  ftp_emb_r           =   ftp_Rebase+'pub/rebase/emboss_r.###' 
66  ############################################################################### 
67  #                   ftp rebase account. 
68  # 
69  #   In order to update the rebase files, Rana need to connect to the 
70  #   ftp server corresponding. 
71  # 
72  #   the general procedure for accessing a ftp server is generally to 
73  #   connect as anonymous user (rebase_name) and providing your e-mail address 
74  #   as password. 
75  # 
76  #   Therefore, you need to enter your e-mail address in rebase_password. 
77  #   The address will not be send to anyone but is necessary to login the 
78  #   ftp server of rebase when connecting as anonymous user. 
79  # 
80  #   Do not forget to enclose the address between "'". 
81  # 
82  Rebase_name         =   'anonymous' 
83  Rebase_password     =   '' 
84  #Rebase_password     =   'your_address@somewhere.something' 
85