#!/usr/bin/perl
use warnings;
use strict;
use WWW::Mechanize;

my $hypermutUrl =
  "http://www.hiv.lanl.gov/content/sequence/HYPERMUT/hypermut.html";
my $mech = WWW::Mechanize->new( autocheck => 1 );

my $alignment_as_string = <<'END_SEQS';
>HIV1-test.CONS
ATGGGATGTCTTGGGAATCAGCTGCTTATCGCGCTCTTGCTAGTAAGTGCTTTAGAGATTTATTGTGTTC
>HIV1-test.1
ATGGAATGTCTTGGAAATCAGCTGCTTATCGCGCTCTTGCTAGTAAGTGCTTTAAAGATTTATTGTGTTC
>HIV1-test.2
ATGGAATGTCTTGGGAATCAGCTGCTTATCGCGCTCTTGCTAGTAAGTGCTTTAAAGATTTATTGTGTTC
END_SEQS

$mech->post(
    $hypermutUrl,
    'FORMAT'            => 'FASTA',
    'ALIGNMENT'         => $alignment_as_string,
    'upfile1'           => '',
    'INN'               => '',
    'OUT'               => '',
    'MUTUPSTREAM'       => '',
    'MUTFROM'           => 'G',
    'MUTTO'             => 'A',
    'MUTDOWNSTREAM'     => 'RD',
    'ENFORCE'           => 'DESCENDANT',
    'CONTROLUPSTREAM'   => '',
    'CONTROLFROM'       => 'G',
    'CONTROLTO'         => 'A',
    'CONTROLDOWNSTREAM' => 'YN|RC',
    'Analysis'          => 'All',
    'submit'            => 'Run',
);

my $page = $mech->content;
open my $FH, ">/tmp/hypermut.html";
print {$FH} $page; close $FH;
warn "saved webpage data to /tmp/hypermut.html\n";