4 comments on “Dig into KEGG 1

  1. Get all the scripts for KEGG
    curl -O http://togows.dbcls.jp/soap/clients/kegg/perl/KeggColorPathwayByElements.pl
    curl -O http://togows.dbcls.jp/soap/clients/kegg/perl/KeggColorPathwayByObjects.pl
    curl -O http://togows.dbcls.jp/soap/clients/kegg/perl/KeggGetBestBestNeighborsByGene.pl
    curl -O http://togows.dbcls.jp/soap/clients/kegg/perl/KeggGetBestNeighborsByGene.pl
    curl -O http://togows.dbcls.jp/soap/clients/kegg/perl/KeggGetCompoundsByEnzyme.pl
    curl -O http://togows.dbcls.jp/soap/clients/kegg/perl/KeggGetCompoundsByPathway.pl
    curl -O http://togows.dbcls.jp/soap/clients/kegg/perl/KeggGetCompoundsByReaction.pl
    curl -O http://togows.dbcls.jp/soap/clients/kegg/perl/KeggGetDrugsByPathway.pl
    curl -O http://togows.dbcls.jp/soap/clients/kegg/perl/KeggGetElementRelationsByPathway.pl
    curl -O http://togows.dbcls.jp/soap/clients/kegg/perl/KeggGetElementsByPathway.pl
    curl -O http://togows.dbcls.jp/soap/clients/kegg/perl/KeggGetEnzymesByCompound.pl
    curl -O http://togows.dbcls.jp/soap/clients/kegg/perl/KeggGetEnzymesByGlycan.pl
    curl -O http://togows.dbcls.jp/soap/clients/kegg/perl/KeggGetEnzymesByPathway.pl
    curl -O http://togows.dbcls.jp/soap/clients/kegg/perl/KeggGetEnzymesByReaction.pl
    curl -O http://togows.dbcls.jp/soap/clients/kegg/perl/KeggGetGenesByKoClass.pl
    curl -O http://togows.dbcls.jp/soap/clients/kegg/perl/KeggGetGenesByOrganism.pl
    curl -O http://togows.dbcls.jp/soap/clients/kegg/perl/KeggGetGenesByPathway.pl
    curl -O http://togows.dbcls.jp/soap/clients/kegg/perl/KeggGetGlycansByEnzyme.pl
    curl -O http://togows.dbcls.jp/soap/clients/kegg/perl/KeggGetGlycansByPathway.pl
    curl -O http://togows.dbcls.jp/soap/clients/kegg/perl/KeggGetGlycansByReaction.pl
    curl -O http://togows.dbcls.jp/soap/clients/kegg/perl/KeggGetHtmlOfColoredPathwayByElements.pl
    curl -O http://togows.dbcls.jp/soap/clients/kegg/perl/KeggGetHtmlOfColoredPathwayByObjects.pl
    curl -O http://togows.dbcls.jp/soap/clients/kegg/perl/KeggGetHtmlOfMarkedPathwayByObjects.pl
    curl -O http://togows.dbcls.jp/soap/clients/kegg/perl/KeggGetLinkdbBetweenDatabases.pl
    curl -O http://togows.dbcls.jp/soap/clients/kegg/perl/KeggGetLinkedPathways.pl
    curl -O http://togows.dbcls.jp/soap/clients/kegg/perl/KeggGetNumberOfGenesByOrganism.pl
    curl -O http://togows.dbcls.jp/soap/clients/kegg/perl/KeggGetParalogsByGene.pl
    curl -O http://togows.dbcls.jp/soap/clients/kegg/perl/KeggGetPathwaysByCompounds.pl
    curl -O http://togows.dbcls.jp/soap/clients/kegg/perl/KeggGetPathwaysByDrugs.pl
    curl -O http://togows.dbcls.jp/soap/clients/kegg/perl/KeggGetPathwaysByEnzymes.pl
    curl -O http://togows.dbcls.jp/soap/clients/kegg/perl/KeggGetPathwaysByGenes.pl
    curl -O http://togows.dbcls.jp/soap/clients/kegg/perl/KeggGetPathwaysByGlycans.pl
    curl -O http://togows.dbcls.jp/soap/clients/kegg/perl/KeggGetPathwaysByReactions.pl
    curl -O http://togows.dbcls.jp/soap/clients/kegg/perl/KeggGetReactionsByCompound.pl
    curl -O http://togows.dbcls.jp/soap/clients/kegg/perl/KeggGetReactionsByEnzyme.pl
    curl -O http://togows.dbcls.jp/soap/clients/kegg/perl/KeggGetReactionsByGlycan.pl
    curl -O http://togows.dbcls.jp/soap/clients/kegg/perl/KeggGetReactionsByPathway.pl
    curl -O http://togows.dbcls.jp/soap/clients/kegg/perl/KeggGetReferencesByPathway.pl
    curl -O http://togows.dbcls.jp/soap/clients/kegg/perl/KeggGetReverseBestNeighborsByGene.pl
    curl -O http://togows.dbcls.jp/soap/clients/kegg/perl/KeggMarkPathwayByObjects.pl
    curl -O http://togows.dbcls.jp/soap/clients/kegg/perl/KeggSearchCompoundsByComposition.pl
    curl -O http://togows.dbcls.jp/soap/clients/kegg/perl/KeggSearchCompoundsByMass.pl
    curl -O http://togows.dbcls.jp/soap/clients/kegg/perl/KeggSearchCompoundsByName.pl
    curl -O http://togows.dbcls.jp/soap/clients/kegg/perl/KeggSearchCompoundsBySubcomp.pl
    curl -O http://togows.dbcls.jp/soap/clients/kegg/perl/KeggSearchDrugsByComposition.pl
    curl -O http://togows.dbcls.jp/soap/clients/kegg/perl/KeggSearchDrugsByMass.pl
    curl -O http://togows.dbcls.jp/soap/clients/kegg/perl/KeggSearchDrugsByName.pl
    curl -O http://togows.dbcls.jp/soap/clients/kegg/perl/KeggSearchDrugsBySubcomp.pl
    curl -O http://togows.dbcls.jp/soap/clients/kegg/perl/KeggSearchGlycansByComposition.pl
    curl -O http://togows.dbcls.jp/soap/clients/kegg/perl/KeggSearchGlycansByKcam.pl
    curl -O http://togows.dbcls.jp/soap/clients/kegg/perl/KeggSearchGlycansByMass.pl
    curl -O http://togows.dbcls.jp/soap/clients/kegg/perl/KeggSearchGlycansByName.pl

  2. http://www.bioinformatics.org/pipermail/bbb/2006-January/002945.html

    #! /usr/bin/env perl
    use SOAP::Lite;
    use CGI qw(:standard);
    use CGI::Carp qw(warningsToBrowser fatalsToBrowser);
    print “Content-type: text/html\r\n\r\n”;
    print ”,
    “\n”;
    print “Kegg test\n”;
    print “\n”;
    #GI number H for human and M for mouse
    #cbl gene
    my $H = 867;
    #jun gene (try $M = 16476 and $H = “”)
    my $M = “”;
    #print “$H : Human
    “;
    $wsdl = ‘http://soap.genome.jp/KEGG.wsdl’;
    #set the soap service
    $serv = SOAP::Lite -> service($wsdl);
    $wsdl = ‘http://soap.genome.jp/KEGG.wsdl’;
    #get the definition of the gene from kegg
    if ($H ) {
    print “$H : Human
    “;
    $keggID = $serv -> btit(‘”‘.”hsa:”.$H.'”‘);
    } elsif ($M) {
    print “$M : Mouse
    “;
    $keggID = $serv -> btit(‘”‘.”mmu:”.$M.'”‘);
    }
    @def = split(/ /,$keggID);
    #kegg id is now in $def[0]
    $genes = SOAP::Data->type(array => [$def[0]]);
    #set colors for the kegg graph
    $fg_list = SOAP::Data->type(array => [‘gray’, ‘#00ff00’, ‘blue’]);
    $bg_list = SOAP::Data->type(array => [‘#ff0000’, ‘yellow’, ‘orange’]);
    #get pathways by genes
    $result = $serv -> get_pathways_by_genes($genes);

    foreach $hit (@{$result}) {
    print “$hit :
    “;
    #get web link to marked static pathways
    $colored = $serv -> mark_pathway_by_objects($hit, $genes);
    #get web link to clickable kegg pathways
    $link = $serv ->
    get_html_of_colored_pathway_by_objects($hit,$genes,$fg_list,$bg_list);
    #print links
    if ($colored or $link) {
    print ““.”“.$colored.”
    .”
    “;
    print ““.”“.$link.”“.”
    “;
    }
    };
    print “Done!
    “;
    print “\n”;

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