Source Code for Package Bio.KEGG

 1  # Copyright 2001 by Tarjei Mikkelsen.  All rights reserved. 
 2  # This code is part of the Biopython distribution and governed by its 
 3  # license.  Please see the LICENSE file that should have been included 
 4  # as part of this package. 
 5   
 6  """ 
 7  This module provides code to work with data from the KEGG database. 
 8   
 9  References: 
10   
11  Kanehisa, M. and Goto, S.; KEGG: Kyoto Encyclopedia of Genes and Genomes. 
12  Nucleic Acids Res. 28, 29-34 (2000). 
13   
14  URL: http://www.genome.ad.jp/kegg/ 
15  """ 
16  KEGG_ITEM_LENGTH = 12 
17  KEGG_LINE_LENGTH = 80 
18  KEGG_DATA_LENGTH = KEGG_LINE_LENGTH - KEGG_ITEM_LENGTH 
19   
20  # wrap rule = [indent, connect, (splitstr, connect, splitafter, keep), ...] 
21  _default_wrap = lambda indent: [indent, "", (" ", "", 1, 0)] 
22   
23   
24 -def _wrap_kegg(line, max_width = KEGG_DATA_LENGTH, wrap_rule = _default_wrap): 
25      """Wraps the input line  for KEGG output. 
26   
27      Arguments: 
28   
29      o info - String holding the information we want wrapped 
30      for KEGG output. 
31      o max_width - Maximum width of a line. 
32      o wrap_rule - A wrap rule (see above) for deciding how to split 
33      strings that must be wrapped. 
34      """ 
35      s = "" 
36      wrapped_line = "" 
37      indent = " " * wrap_rule[0] 
38      connect = wrap_rule[1] 
39      rules = wrap_rule[2:] 
40      while 1: 
41          if len(line) <= max_width: 
42              wrapped_line = wrapped_line + line 
43              s = s + wrapped_line 
44              break 
45          else: 
46              did_split = 0 
47              for rule in rules: 
48                  to = max_width 
49                  if not rule[2]: 
50                      to = to + len(rule[0]) 
51                  split_idx = line.rfind(rule[0], 0, to) 
52                  if split_idx > -1: 
53                      if rule[2] and rule[3]: 
54                          split_idx = split_idx + len(rule[0]) 
55                      wrapped_line = wrapped_line + line[0:split_idx] + "\n" 
56                      if not rule[3]: 
57                          split_idx = split_idx + len(rule[0]) 
58                      line = indent + rule[1] + line[split_idx:] 
59                      did_split = 1 
60                      break 
61              if not did_split: 
62                  wrapped_line = wrapped_line + line[0:max_width] + "\n" 
63                  line = indent + connect + line[max_width:] 
64      return s 
65   
66   
67 -def _write_kegg(item, info, indent = KEGG_ITEM_LENGTH): 
68      """Write a indented KEGG record item. 
69   
70      Arguments: 
71   
72      o item - The name of the item to be written. 
73      o info - The (wrapped) information to write. 
74      o indent - Width of item field. 
75      """ 
76      s = "" 
77      for line in info: 
78          partial_lines = line.splitlines() 
79          for l in partial_lines: 
80              s = s + item.ljust(indent) + l + "\n" 
81              if item is not "":  # ensure item is only written on first line 
82                  item = "" 
83      return s 
84