#!/usr/bin/perl

# clustal2.cgi - a CGI wrapper for running the multiple sequence alignment program clustalw.
# Copyright (C) 1999, Humberto Ortiz Zuazaga.

# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2
# of the License, or (at your option) any later version.

# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.

# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.

use CGI qw(:standard);
use Neuroseq;

# Full path to clustalw
$clustalw = '/usr/local/bin/clustalw';

# Full path to fmtseq sequence formatter.
$fmtseq = '/usr/local/bin/fmtseq';

print Neuroseq::title('ClustalW Multiple Sequence Alignments'),
    'Calls clustalw 1.7 to generate a multiple sequence alignment of submitted nucleotide or amino acid sequence',
    p,
    hr,
    start_form,
    'Enter multiple sequences in any seqio multi-sequence format:',
    p,
    textarea(-name=>'sequence',
                          -default=>'',
                          -rows=>10,
                          -columns=>40),
    p,
    submit,
    reset,
    defaults('Clear'),
    end_form,
    hr;

if (param()) {
    $|=1;			# need this to keep program output in place

    my $sequence = param('sequence');
    my $tmpdir = Neuroseq::mktmpdir("/tmp/clustal2");

    chdir $tmpdir or die "error changing to $tmpdir: $!";

    my $filename = "sequence";
    open (SEQ, ">$filename");
    print SEQ $sequence, "\n";
    close SEQ;
    
    system("$fmtseq -format=fasta -all -output=fasta $filename");
    system("$clustalw -infile=$tmpdir/fasta -align > stdout");

  Neuroseq::printfile("$tmpdir/stdout");
    print hr;
  Neuroseq::printfile("$tmpdir/fasta.aln");
 
    chdir;
  Neuroseq::nukedir($tmpdir);
}

print Neuroseq::footer('1999.05.25');