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