get_kegg_modules.sh

#!/bin/bash

# Copyright (C) <2015> EMBL-European Bioinformatics Institute

# This program is free software: you can redistribute it and/or
# modify it under the terms of the GNU General Public License as
# published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.

# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.

# Neither the institution name nor the name get_kegg_modules can
# be used to endorse or promote products derived from this
# software without prior written permission. For written
# permission, please contact <[email protected]>.

# Products derived from this software may not be called
# get_kegg_modules nor may get_kegg_modules appear in their names
# without prior written permission of the developers.
# You should have received a copy of the GNU General Public
# License along with this program. If not, see
# <http://www.gnu.org/licenses/>.

if [ "$#" -lt 1 ]; then
    echo 'get_kegg_modules KEGG_ORG'
    exit 65
fi

KEGG_ORG=$1

# Get modules
wget --quiet -O modules.txt "http://rest.kegg.jp/list/module/$KEGG_ORG"
# For each module retrieve the genes
for module in $(awk '{print $1}' modules.txt)
do
	wget --quiet -O $(echo $module | awk -F ':' '{print $2}').txt "http://rest.kegg.jp/link/$KEGG_ORG/$module";
	for gene in $(awk -F '\t' '{print $2}' $(echo $module | awk -F ':' '{print $2}').txt | awk -F ':' '{print $2}')
	do
		echo -e "$gene\t$(echo $module | awk -F ':' '{print $2}')";
	done;
	rm $(echo $module | awk -F ':' '{print $2}').txt;
done
# Clean
rm modules.txt