G::SystemsBiology

Pathway

G::Ecell::Pathway - Perl extension for blah blah blah

  use G::Ecell::Pathway;
  blah blah blah

Stub documentation for G::Ecell::Pathway was created by h2xs. It looks like the
author of the extension was negligent enough to leave the stub
unedited.

Blah blah blah.

Methods description

Methods code

    my $self = shift;

    my $filename2=shift;
    my $filename3=shift;
    my $filename1=shift;
    my @RuleFileLine;
    my @HiddenSubstrate;
    my @substrate;
    my @product;
    my @MembraneSubstrate;
    my %WholeProduct;
    my $ProductName;
    my %lhash;
    my @result;

    @HiddenSubstrate=('ACCOA','ADP','AKG','AMP','ATP','CO2','COA','GLN','GLU','NAD','NADH','NADP','NADPH','NH3','PI','PPI','PYR');

    open(SFILE, $filename1)|| die("ERROR: file does not exist\n"); 
    &msg_error("open data file $filename1\n");

    while(<SFILE>){
	@RuleFileLine=split /\t/;
	if($RuleFileLine[0]!~/Type/){
	    push(@substrate,$RuleFileLine[5]) if($RuleFileLine[5]);
	    push(@product,$RuleFileLine[8]) if($RuleFileLine[8]);
	}
    }
    close(SFILE);


    open(SFILE, $filename3)|| die("ERROR: file does not exist\n"); 
    &msg_error("open data file $filename3\n");

    while(<SFILE>){
	@RuleFileLine=split /\t/;
	if($RuleFileLine[0]!~/Type/){
	    push(@MembraneSubstrate,$RuleFileLine[5]) if($RuleFileLine[5]);
	    push(@MembraneSubstrate,$RuleFileLine[8]) if($RuleFileLine[8]);
	}
    }
    close(SFILE); 
    

    open(WFILE, $filename2)|| die("ERROR: file does not exist\n"); 
    &msg_error("open data file $filename2\n");
    
    while(<WFILE>){
	@RuleFileLine=split /\t/;
	if($RuleFileLine[0] eq "REACTOR"){
	    foreach(@RuleFileLine){
		$ProductName=(split /:/)[-1] if(/Product/);
		$WholeProduct{substr($ProductName,0,-2)}=undef;
	    }
	}
    }
    close(WFILE);


    @lhash{@substrate}=undef;
    foreach(@product){
	delete $lhash{$_};
    }
    
    foreach(keys(%WholeProduct)){
	delete $lhash{$_};
    }

    foreach(@MembraneSubstrate){
	delete $lhash{$_};
    }


    @result=keys %lhash;
    return\@ result;

    my $filename=shift;
    my @RuleFileLine;
    my @HiddenSubstrate;
    my @substrate;
    my @product;
    my $ProductName;
    my %lhash;
    my @result;

    @HiddenSubstrate=('ACCOA','ADP','AKG','AMP','ATP','CO2','COA','GLN','GLU','NAD','NADH','NADP','NADPH','NH3','PI','PPI','PYR');


    open(SFILE, $filename)|| die("ERROR: file does not exist\n"); 
##    print STDERR ("open data file $filename\n");

    while(<SFILE>){
	@RuleFileLine=split /\t/;
	if($RuleFileLine[0]!~/Type/){
	    push(@substrate,$RuleFileLine[5]) if($RuleFileLine[5]);
	    push(@product,$RuleFileLine[8]) if($RuleFileLine[8]);
	}
    }
    close(SFILE);


    @lhash{@substrate}=undef;
    foreach(@product){
	delete $lhash{$_};
    }
    
    foreach(@HiddenSubstrate){
	delete $lhash{$_};
    }


    @result=keys %lhash;
    return\@ result;

    my $pkg = shift;
    my $filename = shift;
    my $option = shift;
    my $this;

    return $this;

General documentation

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

perl(1).