#!/usr/bin/perl
#print this MIME data no matter what
print "Content-type: text/html\n\n";
#flush stdout buffer
$| = 1;
&parse_form_data (*data);
#Calculations
use Table;
$loc_data_table = "sc_loc_web";
$scid = $data{'scid'};
$scid =~ s/^\s*(.*?)\s*$/$1/; #get rid of bordering white space
$scid = uc($scid);
#mips id
if (length($scid) == 8) {
$mpid = substr($scid,0,7)."-".substr($scid,7,1);
}
else {$mpid = $scid;} #mips id; hyphens are required for proteins such as YBR084C-A
$scid =~ s/-//g; #remove any hyphens from scid
#first see if the id format is correct
foreach (T_LoadRows ($loc_data_table)) {
if ($_->{"scid_"} eq $scid) {
($pred1,$pred2,$thresh,$thresh_localize,$entropy,$entropy_localize,$cyt,$nuc,$mit,$me2,$en2) = T_GetFields($_,"pred1","pred2","thresh","thresh_localize","entropy","entropy_localize","cyt","nuc","mit","me2","en2"); #our results
($ypd99_orig,$sny99_orig,$sny99_std,$sny99_col,$sny99_qual,$mips_orig,$mips_std,$mips_col,$mips_qual,$sp38_orig,$sp38_std,$sp38_col,$sp38_qual,$spid) = T_GetFields($_,"ypd99_orig","sny99_orig","sny99_std","sny99_col","sny99_qual","mips_orig","mips_std","mips_col","mips_qual","sp38_orig","sp38_std","sp38_col","sp38_qual","spid"); #outside info
last;
}
}
if (not defined $cyt){ #ORF not found
print "The ORF you specified does not exist.";
exit(1);
}
%better_name = ("cyt"=>"cytoplasm", "nuc"=>"nucleus", "mit"=>"mitochondria",
"me2"=>"membrane-related", "en2"=>"ER related", "?"=>"?");
$pred1 = $better_name{$pred1};
$pred2 = $better_name{$pred2};
%collapsed_name = ("cyt"=>"C", "nuc"=>"N", "mit"=>"M",
"me2"=>"T", "en2"=>"E", "-"=>"-", "?"=>"?");
foreach ($sny99_col,$mips_col,$sp38_col) {
$_ = $collapsed_name{$_};
}
%expand = ("y"=>"yes", "n"=>"no");
$thresh_localize = $expand{$thresh_localize};
$entropy_localize = $expand{$entropy_localize};
#SwissProt link line
if ($spid ne "?") {
$sp_link = "Swiss-Prot";
}
else {$sp_link = "Swiss-Prot";}
foreach $item ($cyt,$nuc,$mit,$me2,$en2,$thresh) {
$item = $item/1000;
}
###############################################################################
#CGI Output
#Create html document
print <
Location
HTML
my $hvar = `perl /web/genecensus/header/header.cgi localize`; print $hvar;
print <Localization Prediction
$scid
Predicted Location
Available Resources
| Database
| Collapsed
| Quality
| Standard | Original
|
| Snyder | $sny99_col | $sny99_qual | $sny99_std | $sny99_orig
|
| MIPS | $mips_col | $mips_qual | $mips_std | $mips_orig
|
| $sp_link | $sp38_col | $sp38_qual | $sp38_std | $sp38_orig
|
Localization Quality
| | Value | Well-localized?
|
| Entropy | $entropy | $entropy_localize
|
| Top-two difference | $thresh | $thresh_localize
|
Probability State Vector
| C
| N
| M
| T
| E
|
| $cyt | $nuc | $mit | $me2 | $en2
|
Other Resources
HTML
exit;
sub parse_form_data
{
local (*FORM_DATA) = @_;
local ($request_method, $query_string, @key_value_pairs, $key_value, $key, $value);
$request_method = $ENV{'REQUEST_METHOD'};
if ($request_method eq "GET") {
$query_string = $ENV{'QUERY_STRING'};
} elsif ($request_method eq "POST") {
read(STDIN, $query_string, $ENV{'CONTENT_LENGTH'}); #no. of bytes to receive
} else {
&return_error (500, "Server Error", "Server uses unsupported method");
}
@pairs = split(/&/, $query_string); #making list of keyword-value pair
foreach $pair (@pairs)
{
($key, $value) = split(/=/, $pair);
$value =~ tr/+/ /; #translate "+" to space
#decipher ASCI hexadecimal escaped characters
$value =~ s/%([a-fA-F0-9][a-fA-F0-9])/pack("C", hex($1))/eg;
if (defined ($FORM_DATA{$key})) {
$FORM_DATA{$key} = join ("\0", $FORM_DATA{$key}, $value);
} else {
$FORM_DATA{$key} = $value;
}
}
}
sub return_error
{
local ($status, $keyword, $message) = @_;
print "Content-type: text/html", "\n";
print "Status: ", $status, " ", $keyword, "\n\n";
print <
CGI Program - Unexpected Error
$keyword
$message
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