#! /usr/bin/perl -w

# Thomas Trolle, July 2014
# trolle@cbs.dtu.dk

# Tested on Perl 5.12.4

use CGI qw(:standard);
use strict;

# Define the path to the program that the server should run. 
my $PROG = "/path/to/your/method";

# Parse the input data sent in the URL. Note that 
# the following request format is assumed:
# '<URL>?peptide=<PEPTIDE>&allele=<ALLELE>'
my $query = new CGI;
my $peptide = $query->param('peptide');
my $allele = $query->param('allele');

if ($peptide and $allele) {
    # Check that the input data makes sense.
    if ($peptide !~ m/[ACDEFGHIKLMNPQRSTUVWY,]+/) {
        print "Invalid peptide input\n";
    }

    my @supported_alleles = ("HLA-A*02:01", 
                             "HLA-A*24:02", 
                             "HLA-B*07:02",
                             "HLA-B*08:01");
    
    if ($allele !~ @supported_alleles) {
        print "Invalid allele input\n";
    }

    # Call the program $PROG and save the output in $result
    my $result = `$PROG -mode peptide $allele $peptide`;

    # Parse the output from your program here if necessary. For the 
    # IEDB benchmark, results for each peptide are expected in the 
    # following format: 
    # Allele\tPeptide\tPrediction\n
    print "$result\n";
} 
else {
    print "Please supply some data in the following format: '<URL>?peptide=PEPTIDE&allele=ALLELE'\n";
}