use strict;
use warnings;

use WWW::Mechanize;

my $base_url  = 'http://igs-server.cnrs-mrs.fr/';
my $start_url = $base_url . 'Tcoffee/tcoffee_cgi/index.cgi?action=Make
+%20a%20multiple%20alignment::Advanced&stage1=1';
my $upload    = '/tmp/scratch/dummy.fasta';

my $mech = WWW::Mechanize->new();

$mech->get( $start_url );
$mech->form_number(1);
$mech->set_fields(email => "", -uploaded_file => $upload, -case => "up
+per", -seqnos => "off", -outorder => "input",);
$mech->tick(-in => "Mlalign_id_pair");
$mech->tick(-in => "Mfast_pair");
$mech->tick(-in => "Mclustalw_aln");
$mech->tick(-output => "fasta_aln");
$mech->tick(-output => "score_html");
$mech->submit();

$| = 1;

{
  my $refresh = $mech->res->header( 'refresh' );
  last unless defined $refresh;
  my ( $wait, $rel_url ) = $refresh =~ m,^(\d+)\s*;\s*URL=/(.+)$,;
  die 'match failed' unless defined $wait;
  sleep $wait;
  my $url = $base_url . $rel_url;
  # uncomment the next line if you want to track the progress
  # print "Fetching $url\n";
  $mech->get( $url );
  redo;
}

# at this point, $mech->content should give you the page you want.
my $html = $mech->content;
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