G::Tools::EMBOSS - Wrapper interface to EMBOSS software suite

    This class is a part of G-language Genome Analysis Environment, 
    collecting interfaces to EMBOSS software suite.

    require CGI;
    require LWP::UserAgent;
    require HTML::Form;

    my @args = opt_get(@_);
    my $USA = opt_val("sequence") || shift @args;
    my $feature = opt_val("feature");
    my $firstonly = opt_val("firstonly");
    my $osformat = opt_val("osformat");
    my $help = opt_val("help");
    my $outseq = opt_val("outseq") || shift @args;

    if($help){
	print << '__HELP__'

	   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     (Gapped) sequence(s) filename and optional
                                  format, or reference (input USA)
  [-outseq]            seqoutall  [<sequence>.<format>] Sequence set(s)
                                  filename and optional format (output USA)

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -feature            boolean    Use feature information
   -firstonly          boolean    Read one sequence and stop

   General qualifiers:
   -help               boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
__HELP__
	exit;
    }

    msg_error("Reads and writes (returns) sequences\n");

    if(length($USA) < 1){
	msg_error("Input (gapped) sequence(s): ");
	$USA = <STDIN>;
	chomp($USA);
    }

    unless(length($osformat)){
        if ($USA =~ /(.+)::(.+)/) {
	    ($osformat, $USA) = ($1, $2);
        }
        if ($outseq =~ /(.+)::(.+)/) {
    	    ($osformat, $outseq) = ($1, $2);
        }
        if ($outseq =~ /(.+):(.+)/) {
	    ($osformat, $outseq) = ($1,$2);;
        }
    }

    my $ua = LWP::UserAgent->new;
    my $request = $ua->get("http://emboss.bioinformatics.nl/cgi-bin/emboss/seqret");
    my $form = HTML::Form->parse($request->decoded_content, $request->base);

    if (-e $USA) {
	$form->value("sequence.file","$USA");
    } else {
	$form->value("sequence.db","$USA");
    }

    $form->value('outseq',"${osformat}::outseq") if $osformat;
    $form->value('feature','1') if $feature;
    $form->value('firstonly','1') if $firstonly;

    my $res = $ua->request($form->click('_run'));
    while ($res->is_redirect) {
	my $url = $res->header('Location');
	$res = $ua->request(HTTP::Request->new(GET => $url));
    }

    my $query = CGI->new;
    my $result = $res->content();
    $result =~ m/<pre>(.+)<\/pre>/s;
    $result = $query->unescapeHTML($1);
    while ($result =~ /<pre>/) {
	$result =~ m/^(.+)<\/pre>.+<pre>(.+)/sg;
	$result = "$1\n$2";
    }

    while ($result =~ /Warning/) {
	$result =~ /(Warning.+)/;
	msg_error($1,"\n");
	$result =~ /$1\n+(.+)/s;
	$result = $1;
    }

    if ($result =~ /with -auto/) {
	my @error = split(/:/,$USA);
	msg_error("Error: Failed to open filename\" $error[0]\"\n");
	msg_error("Error: Unable to read sequence\" $USA\"\n");
	msg_error("Died: seqret terminated: Bad value for '-sequence' and no prompt\n");
    } else {
	$result =~ /\s+(.{6})/;
	my $name = $1;
        chomp($name);
	$osformat = "fasta" unless $osformat;
	
	if ($outseq eq "") {
	    msg_error("output sequence(s) [$name.$osformat]: ");
	    $outseq = <STDIN>;
	    chomp($outseq);
	}
	
	if (lc($outseq) eq "stdout") {
	    msg_send("$result\n");
	} elsif ($outseq) {
	    open(RESULT,">$outseq");
	    print RESULT "$result";
	    close(RESULT);
	} else {
	    open(RESULT,">$name.$osformat");
	    print RESULT "$result";
	    close(RESULT);
	}
    }