#! /usr/local/bin/perl

my $header = '/var/web/template.header';
my $footer = '/var/web/template.footer';

print "Content-type: text/html\n\n";

if (open HEADER, "$header") {
        while (<HEADER>) { print $_; }
        close HEADER;
}
else { warn "cannot open $header\n"; }

print <<"ENDHTML1";

<h1><p><center>Welcome to Automatic Blast for 3'UTR!</center></p></h1>
<h3><p>Please fill out the following form!</p></h3>


<form action="blast-5.cgi" enctype="multipart/form-data" method="POST">
<pre>
	Organism: 		<select name="org">
	<option selected>Arabidopsis thaliana [ORGN]</option>
	<option>Aeropyrum pernix [ORGN]</option>
	<option>Aquifex aeolicus [ORGN]</option>	
	<option>Bacillus subtilis [ORGN]</option>
	<option>Bos taurus [ORGN]</option>
	<option>Caenorhabditis elegans [ORGN]</option>
	<option>Danio rerio [ORGN]</option>
	<option>Dictyostelium discoideum [ORGN]</option>
	<option>Drosophila melanogaster [ORGN]</option>
	<option>Escherichia coli [ORGN]</option>
	<option>Gallus gallus [ORGN]</option>
	<option>Homo sapiens [ORGN]</option>
	<option>Human immunodeficiency virus type 1 [ORGN]</option>
	<option>Methanococcus jannaschii [ORGN]</option>
	<option>Mus musculus [ORGN]</option>
	<option>Oryctolagus cuniculus [ORGN]</option>
	<option>Oryza sativa [ORGN]</option>
	<option>Ovis aries [ORGN]</option>
	<option>Plasmodium falciparum [ORGN]</option>
	<option>Rattus norvegicus [ORGN]</option>
	<option>Saccharomyces cerevisiae [ORGN]</option>
	<option>Schizosaccharomyces pombe [ORGN]</option>
	<option>Simian immunodeficiency virus [ORGN]</option>
	<option>Synechocystis PCC6803 [ORGN]</option>
	<option>Takifugu rubripes [ORGN]</option>
	<option>Xenopus laevis [ORGN]</option>
	<option>Zea mays [ORGN]</option>
	<option>Viruses [ORGN]</option>
	<option>Archaea [ORGN]</option>
	<option>Bacteria [ORGN]</option>
	<option>Eukaryota [ORGN]</option>
	<option>Viridiplantae [ORGN]</option>
	<option>Fungi [ORGN]</option>
	<option>Metazoa [ORGN]</option>
	<option>Arthropoda [ORGN]</option>
	<option>Vertebrata [ORGN]</option>
	<option>Mammalia [ORGN]</option>
	<option>Rodentia [ORGN]</option>
	<option>Primates [ORGN]</option>	
	</select>
	Hit Size:
	<input type="radio" name="size" value="10"> 10
	<input type="radio" name="size" value="20" checked> 20
	<input type="radio" name="size" value="40"> 40
	<input type="radio" name="size" value="60"> 60
	<input type="radio" name="size" value="80"> 80
	<input type="radio" name="size" value="100"> 100	
	Email:			<input type="text" name="email"> Make sure your email is correct
	Querry:			<input type="file" name="fasta">(FASTA format only)
	
	<input type="submit" value="Send">      <input type="reset" value="Clear Form">
</pre>
</form>
<h4> 
<p>1. Be patient! Delay is caused by NCBI not by the program itself!</p>
<p>2. You will not get any result if you provide a wrong email address!</p>
<p>3. The query file can contain multiple FASTA format sequences, for example:</p>
</h4>
<h3>
<p>>description</p>
<p>TTAAAGAGATTGAAGAGAAGAAGAGAATCCCTGAGTACTATCCTTATGGTARCCGTGGTCCTGTTGAAGAG</p>
<p>AAGAAGAGAATCCCTGAGTACTATCCTTATGGTARCCGTGAGAATCCCTGAGTACTATCCTTATGGTARCC</p>
<p>GTGGTCCTGTTGAAGAGAAGAAG</p>
<p>>description</p>
<p>TTAAAGAGATTGAAGAGAAGAAGAGAATCCCTGAG</p>
<p>>description</p>
<p>ACTATCCTTATGGTARCCGTGGTCCTGTT</p>
<p>>description</p>
<p>GAAGAAGAGAATCCCTGAGTACTATC</p>
<p></p>
<h4>
<p>4. Please report any problem to <a href = "mailto:xdy\@cs.purdue.edu">Jack Yan</a>.</p>
</h4>

ENDHTML1

if (open FOOTER, "$footer") {
        while (<FOOTER>) { print $_; }
        close FOOTER;
}
else { warn "cannot open $footer\n"; }