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__init__.py
# 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

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