How can you get the path_stat_KO and module_stat_KO?

[SNOWBRO123]

Hi,I wonder that "path_stat_KO" and "module_stat_KO" list are an universal data for the ReporterScore analysis? Or I should construct my own "path_stat_KO" and "module_stat_KO" data acccording to my own data. But how?

[wangpeng407]

Get data from KEGG API, and write a script to generate the same format files.

curl  http://rest.kegg.jp/link/pathway/ko  -o pathway-KO.raw.list
sed 's/ko://g;s/path://g' pathway-KO.raw.list | grep map > pathway-KO.list

curl http://rest.kegg.jp/link/module/ko -o module-KO.raw.list
sed 's/ko://g;s/md://g' module-KO.raw.list > module-KO.list

curl http://rest.kegg.jp/list/module | sed 's/^md://g' > module.desc.list

curl http://rest.kegg.jp/list/pathway | sed 's/^path://g' > pathway.desc.list

perl handle.pl pathway-KO.list pathway.desc.list > path_stat_KO.xls
perl handle.pl module-KO.list module.desc.list > module_stat_KO.xls

handle.pl script

#!/usr/bin/perl -w
use strict;
use warnings;

@ARGV == 2 || die "perl $0 pathway-KO.list pathway.desc.list > path_stat_KO.v2.xls\n";
my ($rlist, $desc) = @ARGV;

my %ID2KOs;

open IN, $rlist || die $!;
while(<IN>){
	chomp;
	my ($KO, $ID) = split /\t/;
	push @{$ID2KOs{$ID}}, $KO;
}
close IN;

print "id\tK_num\tKOs\tDescription\n";
open DESC, $desc || die $!;
while(<DESC>){
	chomp;
	my ($ID, $detail) = split /\t/;
	$ID2KOs{$ID} || warn "No KOs in $ID\n";
	$ID2KOs{$ID} || next;
	print "$ID\t", scalar(@{$ID2KOs{$ID}}), "\t", join(",", @{$ID2KOs{$ID}}), "\t", $detail, "\n";
}
close DESC;