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# Copyright 2001 by Tarjei Mikkelsen. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""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
def _default_wrap(indent):
"""Return default wrap rule for _wrap_kegg (PRIVATE).
A wrap rule is a list with the following elements:
[indent, connect, (splitstr, connect, splitafter, keep), ...]
"""
return [indent, "", (" ", "", 1, 0)]
def _struct_wrap(indent):
"""Return wrap rule for KEGG STRUCTURE (PRIVATE)."""
return [indent, "", (" ", "", 1, 1)]
def _wrap_kegg(line, max_width=KEGG_DATA_LENGTH, wrap_rule=_default_wrap):
"""Wrap the input line for KEGG output (PRIVATE).
Arguments:
- info - String holding the information we want wrapped
for KEGG output.
- max_width - Maximum width of a line.
- 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 True:
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 (PRIVATE).
Arguments:
- item - The name of the item to be written.
- info - The (wrapped) information to write.
- indent - Width of item field.
"""
s = ""
for line in info:
partial_lines = line.splitlines()
for partial in partial_lines:
s += item.ljust(indent) + partial + "\n"
if item: # ensure item is only written on first line
item = ""
return s
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