None available.
sub enzyme_layout
{ &opt_default(output=>"show",filename=>"enzyme_layout.txt", limit=>30);
my @args = opt_get(@_);
my $filename = shift @args;
my $output = opt_val("output");
my $outfile = opt_val("filename");
my $limit = opt_val("limit");
my @contents;
my %RuleHash;
my $word;
my $number=1;
my $s=1;
my $p=1;
my $e=1;
my %Interaction;
my %sum;
open(FILE, $filename)|| die("ERROR: file does not exist\n");
&msg_error("open data file $filename\n");
while(<FILE>){
my @substrate=();
my @product=();
my @enzyme=();
tr/\n//d;
@contents=split /\t/;
if($contents[0] eq 'REACTOR'){
$s=$p=$e=1;
$RuleHash{$number}{Type}=shift(@contents);
$RuleHash{$number}{Class}=shift(@contents);
($RuleHash{$number}{Path},$RuleHash{$number}{ID})=split(/:/,shift(@contents));
$RuleHash{$number}{Name}=shift(@contents);
$RuleHash{$number}{Enzyme}=(split(/ /,$RuleHash{$number}{Name}))[2];
foreach $word (@contents){
if($word=~/Substrate/){
($RuleHash{$number}{"S_path$s"},$RuleHash{$number}{"S_ID$s"})=split(/:/,(split(/ /,$word))[1]);
$sum{$RuleHash{$number}{"S_ID$s"}}++;
push(@substrate,$RuleHash{$number}{"S_ID$s"});
$RuleHash{$number}{"S_Coeff$s"}=(split(/ /,$word))[2];
$s++;
}elsif($word=~/Product/){
($RuleHash{$number}{"P_path$p"},$RuleHash{$number}{"P_ID$p"})=split(/:/,(split(/ /,$word))[1]);
$sum{$RuleHash{$number}{"P_ID$p"}}++;
push(@product,$RuleHash{$number}{"P_ID$p"});
$RuleHash{$number}{"P_Coeff$p"}=(split(/ /,$word))[2];
$p++;
}elsif($word=~/Effector/){
($RuleHash{$number}{"E_path$e"},$RuleHash{$number}{"E_ID$e"})=split(/:/,(split(/ /,$word))[1]);
$RuleHash{$number}{"E_Coeff$e"}=(split(/ /,$word))[2];
$e++;
}elsif($word=~/Catalyst/){
($RuleHash{$number}{C_path},$RuleHash{$number}{C_ID})=split(/:/,(split(//,$word))[1]);
}else{
$RuleHash{$number}{Arg_tag}{(split(/ /,$word))[0]}=(split(/ /,$word))[1];
}
}
$Interaction{$number}{substrate} =\@ substrate;
$Interaction{$number}{product} =\@ product;
$Interaction{$number}{enzyme} = $RuleHash{$number}{Enzyme};
$number++;
}
if($contents[0] eq 'Include'){
$RuleHash{$number}{Type}=shift(@contents);
$RuleHash{$number}{Class}=shift(@contents);
}
}
foreach my $key (keys(%sum)){
if($sum{$key} > $limit){
print "DELETED $sum{$key} $key\n";
}
}
open (OUTFILE,">$outfile");
for(my $num=0; $num<$number-1; $num++){
for(my $pro = 0; $pro <= $#{$Interaction{$num}{product}}; $pro++){
my $product = ${$Interaction{$num}{product}}[$pro];
if( $sum{$product} < $limit){
for(my $others=0; $others<$number-1; $others++){
if($num != $others){
for(my $sub=0; $sub <= $#{$Interaction{$others}{substrate}}; $sub++){
my $substrate = ${$Interaction{$others}{substrate}}[$sub];
if($sum{$substrate}<$limit){
if($product eq $substrate){
print OUTFILE "$Interaction{$num}{enzyme} $Interaction{$others}{enzyme}\n";
}
}
}
}
}
}
}
}
close OUTFILE;
if($output eq "show"){
system "java -jar /usr/local/bin/biolayout.jar $outfile";
}} | sub substance_layout
{ &opt_default(output=>"show",filename=>"substance_layout.txt", limit=>30);
my @args = opt_get(@_);
my $filename = shift @args;
my $output = opt_val("output");
my $outfile = opt_val("filename");
my $limit = opt_val("limit");
my @contents;
my %RuleHash;
my $word;
my $number=1;
my $s=1;
my $p=1;
my $e=1;
my %Interaction;
my %sum;
open(FILE, $filename)|| die("ERROR: file does not exist\n");
&msg_error("open data file $filename\n");
while(<FILE>){
my @substrate=();
my @product=();
my @enzyme=();
tr/\n//d;
@contents=split /\t/;
if($contents[0] eq 'REACTOR'){
$s=$p=$e=1;
$RuleHash{$number}{Type}=shift(@contents);
$RuleHash{$number}{Class}=shift(@contents);
($RuleHash{$number}{Paeth},$RuleHash{$number}{ID})=split(/:/,shift(@contents));
$RuleHash{$number}{Name}=shift(@contents);
$RuleHash{$number}{Enzyme}=(split(/ /,$RuleHash{$number}{Name}))[2];
foreach $word (@contents){
if($word=~/Substrate/){
($RuleHash{$number}{"S_path$s"},$RuleHash{$number}{"S_ID$s"})=split(/:/,(split(/ /,$word))[1]);
$sum{$RuleHash{$number}{"S_ID$s"}}++;
push(@substrate,$RuleHash{$number}{"S_ID$s"});
$RuleHash{$number}{"S_Coeff$s"}=(split(/ /,$word))[2];
$s++;
}elsif($word=~/Product/){
($RuleHash{$number}{"P_path$p"},$RuleHash{$number}{"P_ID$p"})=split(/:/,(split(/ /,$word))[1]);
$sum{$RuleHash{$number}{"P_ID$p"}}++;
push(@product,$RuleHash{$number}{"P_ID$p"});
$RuleHash{$number}{"P_Coeff$p"}=(split(/ /,$word))[2];
$p++;
}elsif($word=~/Effector/){
($RuleHash{$number}{"E_path$e"},$RuleHash{$number}{"E_ID$e"})=split(/:/,(split(/ /,$word))[1]);
$RuleHash{$number}{"E_Coeff$e"}=(split(/ /,$word))[2];
$e++;
}elsif($word=~/Catalyst/){
($RuleHash{$number}{C_path},$RuleHash{$number}{C_ID})=split(/:/,(split(/ /,$word))[1]);
}else{
$RuleHash{$number}{Arg_tag}{(split(/ /,$word))[0]}=(split(/ /,$word))[1];
}
}
$Interaction{$number}{substrate} =\@ substrate;
$Interaction{$number}{product} =\@ product;
$Interaction{$number}{enzyme} = $RuleHash{$number}{Enzyme};
$number++;
}
if($contents[0] eq 'Include'){
$RuleHash{$number}{Type}=shift(@contents);
$RuleHash{$number}{Class}=shift(@contents);
}
}
foreach my $key (keys(%sum)){
if($sum{$key} > $limit){
print "DELETED $sum{$key} $key\n";
}
}
open (OUTFILE,">$outfile");
for(my $num=0; $num<$number-1; $num++){
for(my $sub=0; $sub<=$#{$Interaction{$num}{substrate}}; $sub++){
my $substrate = ${$Interaction{$num}{substrate}}[$sub];
if($sum{$substrate}<$limit){
for(my $pro=0; $pro<=$#{$Interaction{$num}{product}}; $pro++){
my $product = ${$Interaction{$num}{product}}[$pro];
if($sum{$product}<$limit){
print OUTFILE "$substrate $product\n";
}
}
}
}
}
close OUTFILE;
if($output eq "show"){
system "java -jar /usr/local/bin/biolayout.jar $outfile";
}} |