G::SystemsBiology
Interaction
G::Ecell::Interaction - Perl extension for blah blah blah
|
| Globals (from use vars definitions) |
| @EXPORT |
| $VERSION |
| @EXPORT_OK |
| Privates (from my definitions) |
| %substance_list; |
| $product = ${$Interaction{$num}{product}}[$pro] |
| $printinteraction = '' |
| %COG_fcode = ( J=>"Translation, ribosomal structure and biogenesis", K=>"Transcription", L=>"DNA replication, recombination and repair", D=>"Cell division and chromosome partitioning", O=>"Posttranslational modification, protein turnover, chaperones", M=>"Cell envelope biogenesis, outer membrane", N=>"Cell motility and secretion", P=>"Inorganic ion transport and metabolism", T=>"Signal transduction mechanisms", C=>"Energy production and conservation", G=>"Carbohydrate transport and metabolism", E=>"Amino acid transport and metabolism", F=>"Nucleotide transport and metabolism", H=>"Coenzyme metabolism", I=>"Lipid metabolism", Q=>"Secondary metabolites biosynthesis, transport and catabolism", R=>"General function prediction only", S=>"Function unknown", '-'=>"Non COG" ) |
| $substrate = ${$Interaction{$num}{substrate}}[$sub] |
use G::Ecell::Interaction;
blah blah blah
|
Stub documentation for G::Ecell::Interaction was created by h2xs. It looks like the
author of the extension was negligent enough to leave the stub
unedited.
Blah blah blah.
|
| DESTROY | No description | Code |
| new | No description | Code |
| substance_layout2 | No description | Code |
Methods description
Methods code
sub DESTROY
{ my $self = shift;
}
sub new
{ my $pkg = shift;
my $filename = shift;
my $option = shift;
my $this;
return $this;}
| substance_layout2 | description | top | prev | next |
sub substance_layout2
{ &opt_default(output=>"show",filename=>"layout2.html", ptt=>"");
my @args = opt_get(@_);
my $gb = shift @args;
my $filename = shift @args;
my $output = opt_val("output");
my $outfile = opt_val("filename");
my $ptt = opt_val("ptt");
set_gpac($gb, -ptt=>$ptt);
my %gene2id;
foreach my $cds ($gb->cds()){
$gene2id{$gb->{$cds}->{gene}} = $cds;
}
mkdir("graph", 0777);
open(FILE, '>graph/' . $outfile);
print FILE qq(
<html>
<head>
<title>GENESYS: Substance Layout</title>
</head>
<body>
<applet code="GraphInteraction.class" width=800 height=600>
); ##"
print FILE '<param name=functionkey value="';
my $printcode = '';
foreach my $code (keys %COG_fcode){
$printcode .= sprintf("%s\#%s,", $code, $COG_fcode{$code});
}
print FILE $printcode . '">' . "\n"; ##"
my @contents;
my %RuleHash;
my $word;
my $number=1;
my ($s, $p, $e) = (1,1,1);
my %Interaction;
my %sum;
open(ERI, $filename)|| die("ERROR: file does not exist\n");
while(<ERI>){
my @substrate=();
my @product=();
my @enzyme=();
tr/\n//d;
@contents=split /\t/;
if($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}{ID}))[0];
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);
}
}
close(ERI);
my $printinter = '';
print FILE qq(<param name=interaction value=");
for(my $num=0; $num<$number-1; $num++){
for(my $sub=0; $sub<=$##{$Interaction{$num}{substrate}}; $sub++){
my $substrate = ${$Interaction{$num}{substrate}}[$sub];
for(my $pro=0; $pro<=$##{$Interaction{$num}{product}}; $pro++){
my $product = ${$Interaction{$num}{product}}[$pro];
$printinter .= "$substrate-$product,";
}}
General documentation