Sending data over to another Script at the click of a button!

#!/usr/bin/perl -w
use CGI::Carp 'fatalsToBrowser';
# ORFfinder.pl
# Perl programme to read in FastA format to find all possible open
# reading frames (ORFS) beginning with ATG and ending with a stop codon,
# TGA, TAA, TAG)
 
# Analyse all six open reading frames and predict ORFS in all six. Only
# longest ORF will be used.
 
require 'module.pm';
use CGI;
use strict;
use warnings;
use DNALib;
use ReadingFrameModules;
my $query = new CGI;
 
# Initialise variables
my ($dna, $dna1, $dna2, $dna3, $dna5, $dna6, $revcom, $revcom1, $revcom2, $longorf1, $longorf2, $longorf3, $longorf4, $longorf5, $longorf6, 
$dna_filename);
$dna=$dna1=$dna2=$dna3=$dna5=$dna6=$revcom=$revcom1=$revcom2=$longorf1=$longorf2=$longorf3=$longorf4=$longorf5=$longorf6=$dna_filename='';
my $dna_file;
my @file_data;
my $dna_header;
 
   # If a text box provided, take from that
if ($query->param('dna-textbox')) {
   $dna1 = $query->param('dna-textbox');
   # take header and save it as a string $dna_header
   ($dna_header, $dna1) = split(/\n/, $dna1, 2);
 
   $dna = extract_string_sequence_from_fasta_data($dna1);
 }
   # Else see if file upload
elsif($query->param('fileupload'))  {
 
   #  Retrieve the file from the web post instead of the filesystem
  @file_data = get_file_data();
   #Extract the sequence from the contents of the file
   $dna = extract_sequence_from_fasta_data(@file_data);
}
 
 
# Add ACGT Validation, changing all non ACGT code to A
$dna =~ s/[^acgt]/a/g;
 
 
# feed the dna data into open_reading_frame to return the longest ORF
 
$longorf1 = open_reading_frame($dna);
 
# remove first base from sequence
$dna2 = substr $dna, 1;
$longorf2 = open_reading_frame($dna2);
 
# remove first base from $dna2
$dna3 = substr $dna2, 1;
$longorf3 = open_reading_frame($dna3);
 
#Reverse compliment the DNA sequence
$revcom = revcom($dna);
$longorf4 = open_reading_frame($revcom);
 
 
#remove first base from sequence
$dna5 = substr $revcom, 1;
$longorf5 = open_reading_frame($dna5);
 
#remove a further base from the sequence
$dna6 = substr $dna5, 1;
$longorf6 = open_reading_frame($dna6);
 
# SECOND HALF OF THE PROGRAM - THIS WAS ORIGINALLY TO BE SENT TO A SECOND SCRIPT
# FOR TASK 2 BUT HAD PROBLEMS WITH THE CGI IMPLEMENTING TWO SCRIPTS ON ONE HTML FORM
 
# my($longorf1,$longorf2,$longorf3,$longorf4,$longorf5,$longorf6)=@ARGV;
 
#Transfer Open Reading Frames over to ProteinDigest
# system './proteindigest.pl', $longorf1,$longorf2,$longorf3,$longorf4,$longorf5,$longorf6;
 
# Initialise second program variables
my $orfprotein1 = '';
my $orfprotein2 = '';
my $orfprotein3 = '';
my $orfprotein4 = '';
my $orfprotein5 = '';
my $orfprotein6 = '';
my $codon;
 
# Convert DNA sequence to Protein sequence - Translate each three base
# codon into an amino acid, and append to the protein
 
for(my $i=0; $i < (length($longorf1) -2) ; $i += 3) {
$codon = substr($longorf1,$i,3);
$orfprotein1 .= codon2aa($codon);
}
 
for(my $i=0; $i < (length($longorf2) -2) ; $i += 3) {
$codon = substr($longorf2,$i,3);
$orfprotein2 .= codon2aa($codon);
}
 
for(my $i=0; $i < (length($longorf3) -2) ; $i += 3) {
$codon = substr($longorf3,$i,3);
$orfprotein3 .= codon2aa($codon);
}
 
for(my $i=0; $i < (length($longorf4) -2) ; $i += 3) {
$codon = substr($longorf4,$i,3);
$orfprotein4 .= codon2aa($codon);
}
 
for(my $i=0; $i < (length($longorf5) -2) ; $i += 3) {
$codon = substr($longorf5,$i,3);
$orfprotein5 .= codon2aa($codon);
}
 
for(my $i=0; $i < (length($longorf6) -2) ; $i += 3) {
$codon = substr($longorf6,$i,3);
$orfprotein6 .= codon2aa($codon);
}
 
# Add N-terminal to each reading frame
 
$orfprotein1 = $orfprotein1 = "_$orfprotein1";
$orfprotein2 = $orfprotein2 = "_$orfprotein2";
$orfprotein3 = $orfprotein3 = "_$orfprotein3";
$orfprotein4 = $orfprotein4 = "_$orfprotein4";
$orfprotein5 = $orfprotein5 = "_$orfprotein5";
$orfprotein6 = $orfprotein6 = "_$orfprotein6";
 
 
 
 
 
 
 
 
 
my $enzyme = $query->param('enzyme');
 
# Select an enzyme from the radio buttons on form
my $re;
if   ($enzyme eq   'TRYPSIN') { $re=qr/(?<=[KR])(?!P)/; }
elsif($enzyme eq 'ENDOPROTL') { $re=qr/(?<=K)(?!P)/; }
elsif($enzyme eq 'ENDOPROTA') { $re=qr/(?<=R)(?!P)/; }
elsif($enzyme eq    'V8PROT') { $re=qr/(?<=E)(?!P)/; }
else {die "Unknown enzyme selection '$enzyme'\n";}
 
 
# To cleave all proteins, and put then in the same array
my @parts;
foreach my $seq ($orfprotein1,$orfprotein2,$orfprotein3,$orfprotein4,$orfprotein5,$orfprotein6) {
    push @parts, split($re, $seq);
}
 
# Now, @parts contains everything
# Generate an array of all digested protein fragments
my @fragments = join("<br>\n", @parts); 
 
print "Content-type:  text/html
 
<html>
<head>
<link href='thrColElsHdr.css' rel='stylesheet' type='text/css' />
</head>
<div class='thrColElsHdr'>
 
<div id='container'>
  <div id='header'>
     
     <img src='dna.png' alt='DNA double helix' />
 
         <h2>Peptide mass/charge analyser</h2>
 
 
    
 
    
  <!-- end #header --></div>
  <div id='sidebar1'>
  
  <!-- end #sidebar1 --></div>
  <div id='sidebar2'>
  
  <!-- end #sidebar2 --></div>
  <div id='mainContent'>
  
  <form id='form2' name='form2' method='post' action='save.pl'>
 
<h2>Protein Digestion Results for $dna_header</h2>
<form method= 'link' action='save.pl'>
<label>To Save this data to a text file, Click Here:  <input class='form-button' type='submit' value='Save Results'>
 
</label>
</form>
<form id='form3' name='form3' method='post' action='mass.pl'>
<label>Please select a Mass to be analysed before continuing to the mass 
analyser:<br />    <br />
    <label>
      <input type='radio' name='mass' value='average' 
id='average' />
      Average</label>
    <label>
      <input type='radio' name='mass' value='mono-isotopic' 
id='mono-isotopic'
/>
      Mono-Isotopic</label>
    <br />
<br />
 
Please click here:
<form method= 'link' action='mass.pl'> <input class='form-button' type='submit' value='M/Z Analyser'>
 
</form>
 
<hr />
 
<p>List of protein cleavage fragments, cleaved with enzyme $enzyme;</p>
<p>@fragments</p>  
 
  
  
  
  
 
 
 
 
 
	<!-- end #mainContent --></div>
	<!-- This clearing element should immediately follow the #mainContent div in order to force the #container div to contain all child floats --><br class='clearfloat' />
   <div id='footer'>
<p><a href='Help.pl#references'>REFERENCES</a> | <a href='Help.pl#about'>ABOUT</a></p>
  <!-- end #footer --></div>
<!-- end #container --></div>
</div>
</html>
 
";

Select allOpen in new window