Hi, I think you could use the APIs in KEGG.For example to get the total numbers of genes in hsa00010.The code is written in Perl:
#!/usr/bin/env perl
use SOAP::Lite +trace => [qw(debug)];
my $serv = SOAP::Lite -> service("http://soap.genome.jp/KEGG.wsdl");
my $result = $serv->get_genes_by_pathway('path:hsa00010');
my $count = 0;
foreach (@{$result}){
print $_,"\n";
$count += 1;
}
print $count,"\n";
The answer is 65.
KEGG now operates with REST instead of SOAP. Could be done in a feasible way. But I did this:
wget -O http://rest.kegg.jp/link/pathway/hsa >HSA.txt ##Saving the file
cut -d " " -f 2 HSA.txt | cut -d ":" -f 2 | sort -u | wc -l ## counting the pathways in Human
283 (pathways in Human in KEGG at present)
~Prakki Datta
Yes, this is the correct number of pathways for human in KEGG and it is also the right way to find them.
Many thanks. I've a further question: for a particular pathway like http://www.genome.jp/dbget-bin/www_bget?pathway+hsa00010, I wish to get the total no. of genes involved in that pathway. Is there an easy way to find it? Thanks in advance.
You are correct. The answer now is 260.
You can also use perl script to do this:
#!/usr/bin/env perl
use SOAP::Lite;
$wsdl = 'http://soap.genome.jp/KEGG.wsdl';
$results = SOAP::Lite
-> service($wsdl)
-> list_pathways("hsa");
my $file_name = "kegg_hsa_pathways.txt";
if (open (OUTFILE, '>'.$file_name))
{
foreach $path (@{$results}) {
print OUTFILE "$path->{entry_id}\t$path->{definition}\n";
}
close(OUTFILE);
print "Content writtent to $file_name!"
}
else{
die "Error: Error occur in writing to file\n";
}
If you need their graphs, I generated them in dot format.
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Many Thanks !!!!
+1 for KEGG API, that's a neat resource !