Summary

G::Tools::KEGG_API3 - Perl extension for blah blah blah

Package variables

Included modules

Inherit

Exporter

Synopsis

  use G::Tools::KEGG_API3;
  blah blah blah

Description

Stub documentation for G::Tools::KEGG_API3 was created by h2xs. It looks like the
author of the extension was negligent enough to leave the stub
unedited.
Blah blah blah.

Methods

Methods description

None available.

Methods code

sub bfind {

 shift @_;
 my $response = SOAP::Lite->service("$url")->bfind(@_);
 return $response;

}

sub bget {

 shift @_;
 my $response = SOAP::Lite->service("$url")->bget(@_);
 return $response;

}

sub binfo {

 shift @_;
 my $response = SOAP::Lite->service("$url")->binfo(@_);
 return $response;

}

sub btit {

 shift @_;
 my $response = SOAP::Lite->service("$url")->btit(@_);
 return $response;

}

sub color_pathway_by_objects {

    my @input;
    my @cpd;
    my @enz;
    my @genes;
    my @filename;
    shift @_;
    my $pathway = shift(@_);
    my $obj = shift(@_);
    my $fg = shift(@_);
    my $bg = shift(@_);
    my $spi = shift(@_); 
    my $show = shift(@_);

    $spi =~ s/-//g;
    foreach my $list (@{$obj}){
	if($list =~ /^C[0-9]+/){
	    push(@cpd,"cpd:$list");
	    push(@input,"cpd:$list");
	}
	elsif($list =~ /^[0-9]+\.[0-9]+\./){
	    push(@enz,"ec:$list");
	    push(@input,"ec:$list");
	}
	else{
	    push(@genes,"$spi:$list");
	    push(@input,"$spi:$list");
	}
    }

    my $data_genes = SOAP::Data->type(array=>[@genes]);
    my $data_enz = SOAP::Data->type(array=>[@enz]);
    my $data_cpd = SOAP::Data->type(array=>[@cpd]);
    my $data_a = SOAP::Data->type(array=>[@input]);
    my $data_b = SOAP::Data->type(array=>[@{$fg}]);
    my $data_c = SOAP::Data->type(array=>[@{$bg}]);

    my %res;
    my $num;
    if(length $pathway){
	%res = ($pathway, 1);
    }else{
	my $response_genes = SOAP::Lite->service("$url")->get_pathways_by_genes($data_genes);
	my $response_enz = SOAP::Lite->service("$url")->get_pathways_by_enzymes($data_enz);
	my $response_cpd = SOAP::Lite->service("$url")->get_pathways_by_compounds($data_cpd);
	my $count = 0;
	my $num = 0;
	foreach my $gene_res (@{$response_genes}){
	    $res{$gene_res}++;
	    if($gene_res){
		$count = 1;
	    }
	}
	if($count == 1){$num++}
	foreach my $enz_res (@{$response_enz}){
	    $res{$enz_res}++;
	    if($enz_res){
		$count = 2;
	    }
	}
	if($count == 2){$num++}
	foreach my $cpd_res (@{$response_cpd}){
	    $cpd_res =~ s/PATH: /path:/g;
	    $res{$cpd_res}++;
	    if($cpd_res){
		$count = 3;
	    }
	}
	if($count == 3){$num++}
    }

    mkdir("graph", 0777);
    chdir("graph");
    foreach my $pathway_in (keys(%res)){
	msg_error "searching object in pathway->$pathway_in\n";
	if($res{$pathway_in} >= $num){
	    my $response = SOAP::Lite->service("$url")->color_pathway_by_objects($pathway_in,$data_a,$data_b,$data_c);
	    system("wget $response");
	    my @array = split(/:/,$pathway_in);
	    push(@filename,"$array[1].gif");
	}
    }
    unless($show){
	foreach my $name (@filename){
	    msg_gimv($name);
	}
    }
    chdir("../");

    return @filename;

}

sub get_best_best_neighbors_by_gene {

 shift @_;
 my $response = SOAP::Lite->service("$url")->get_best_best_neighbors_by_gene(@_);
 return $response;

}

sub get_best_neighbors_by_gene {

 shift @_;
 my $response = SOAP::Lite->service("$url")->get_best_neighbors_by_gene(@_);
 return $response;

}

sub get_compounds_by_enzyme {

 shift @_;
 my $response = SOAP::Lite->service("$url")->get_compounds_by_enzyme(@_);
 return $response;

}

sub get_compounds_by_pathway {

 shift @_;
 my $response = SOAP::Lite->service("$url")->get_compounds_by_pathway(@_);
 return $response;

}

sub get_compounds_by_reaction {

 shift @_;
 my $response = SOAP::Lite->service("$url")->get_compounds_by_reaction(@_);
 return $response;

}

sub get_enzymes_by_compound {

 shift @_;
 my $response = SOAP::Lite->service("$url")->get_enzymes_by_compound(@_);
 return $response;

}

sub get_enzymes_by_gene {

 shift @_;
 my $response = SOAP::Lite->service("$url")->get_enzymes_by_gene(@_);
 return $response;

}

sub get_enzymes_by_pathway {

 shift @_;
 my $response = SOAP::Lite->service("$url")->get_enzymes_by_pathway(@_);
 return $response;

}

sub get_enzymes_by_reaction {

 shift @_;
 my $response = SOAP::Lite->service("$url")->get_enzymes_by_reaction(@_);
 return $response;

}

sub get_genes_by_enzyme {

 shift @_;
 my $response = SOAP::Lite->service("$url")->get_genes_by_enzyme(@_);
 return $response;

}

sub get_genes_by_motifs {

 shift @_;
 my $max = pop(@_);
 my $start = pop(@_);
 my $data_a = SOAP::Data->type(array=>[@_]);
 my $response = SOAP::Lite->service("$url")->get_genes_by_motifs($data_a,$start,$max);
 return $response;

}

sub get_genes_by_organism {

 shift @_;
 my $response = SOAP::Lite->service("$url")->get_genes_by_organism(@_);
 return $response;

}

sub get_genes_by_pathway {

    shift @_;
    my $response = SOAP::Lite->service("$url")->get_genes_by_pathway(@_);
    return $response;

}

sub get_ko_by_gene {

 shift @_;
 my $response = SOAP::Lite->service("$url")->get_ko_by_gene(@_);
 return $response;

}

sub get_ko_members {

 shift @_;
 my $response = SOAP::Lite->service("$url")->get_ko_members(@_);
 return $response;

}

sub get_linkdb_by_entry {

 shift @_;
 my $response = SOAP::Lite->service("$url")->get_linkdb_by_entry(@_);
 return $response;

}

sub get_linked_pathways {

 shift @_;
 my $response = SOAP::Lite->service("$url")->get_linked_pathways(@_);
 return $response;

}

sub get_motifs_by_gene {

 shift @_;
 my $response = SOAP::Lite->service("$url")->get_motifs_by_gene(@_);
 return $response;

}

sub get_neighbors_by_gene {

 shift @_;
 my $response = SOAP::Lite->service("$url")->get_neighbors_by_gene(@_);
 return $response;

}

sub get_number_of_genes_by_organism {

 shift @_;
 my $response = SOAP::Lite->service("$url")->get_number_of_genes_by_organism(@_);
 return $response;

}

sub get_oc_members_by_gene {

 shift @_;
 my $response = SOAP::Lite->service("$url")->get_oc_members_by_gene(@_);
 return $response;

}

sub get_paralogs_by_gene {

 shift @_;
 my $response = SOAP::Lite->service("$url")->get_paralogs_by_gene(@_);
 return $response;

}

sub get_pathways_by_compounds {

 shift @_;
 my $in = shift(@_);
 my $data_a = SOAP::Data->type(array=>[@{$in}]); 
 my $response = SOAP::Lite->service("$url")->get_pathways_by_compounds($data_a);
 return $response;

}

sub get_pathways_by_enzymes {

 shift @_;
 my $in = shift(@_);
 my $data_a = SOAP::Data->type(array=>[@{$in}]); 
 my $response = SOAP::Lite->service("$url")->get_pathways_by_enzymes($data_a);
 return $response;

}

sub get_pathways_by_genes {

 shift @_;
 my $in = shift(@_);
 my $data_a = SOAP::Data->type(array=>[@{$in}]);
 my $response = SOAP::Lite->service("$url")->get_pathways_by_genes($data_a);
 return $response;

}

sub get_pathways_by_reactions {

 shift @_;
 my $in = shift(@_);
 my $data_a = SOAP::Data->type(array=>[@{$in}]); 
 my $response = SOAP::Lite->service("$url")->get_pathways_by_reactions($data_a);
 return $response;

}

sub get_pc_members_by_gene {

 shift @_;
 my $response = SOAP::Lite->service("$url")->get_pc_members_by_gene(@_);
 return $response;

}

sub get_reactions_by_compound {

 shift @_;
 my $response = SOAP::Lite->service("$url")->get_reactions_by_compound(@_);
 return $response;

}

sub get_reactions_by_enzyme {

 shift @_;
 my $response = SOAP::Lite->service("$url")->get_reactions_by_enzyme(@_);
 return $response;

}

sub get_reactions_by_pathway {

 shift @_;
 my $response = SOAP::Lite->service("$url")->get_reactions_by_pathway(@_);
 return $response;

}

sub get_reverse_best_neighbors_by_gene {

 shift @_;
 my $response = SOAP::Lite->service("$url")->get_reverse_best_neighbors_by_gene(@_);
 return $response;

}

sub get_similarity_between_genes {

 shift @_;
 my $response = SOAP::Lite->service("$url")->get_similarity_between_genes(@_);
 return $response;

}

sub list_databases {

 shift @_;
 my $response = SOAP::Lite->service("$url")->list_databases(@_);
 return $response;

}

sub list_organisms {

 shift @_;
 my $response = SOAP::Lite->service("$url")->list_organisms(@_);
 return $response;

}

sub list_pathways {

 shift @_;
 my $response = SOAP::Lite->service("$url")->list_pathways(@_);
 return $response;

}

sub load_kegg_api {

    my $pkg = shift;
    my $self = {};
    return bless ($self,$pkg);

}

sub mark_pathway_by_objects {

 shift @_;
 my $pathway = shift(@_);
 my $in = shift(@_);
 my $data_a = SOAP::Data->type(array=>[@{$in}]);
 my $response = SOAP::Lite->service("$url")->mark_pathway_by_objects($pathway,$data_a);
 system("wget -q $response");
 my @array = split(/:/,$pathway);
 system("display  $array[1].gif");
 return $response;

}

General documentation

A. U. Thor, a.u.thor@a.galaxy.far.far.away

perl(1).