#!@WHICHPERL@ -w
#
# $Id:$
#
# FILE: iupac2meme
# AUTHOR: Timothy L. Bailey
# CREATE DATE: 3/06/2010
# DESCRIPTION: Convert a DNA IUPAC motif to MEME format 

use warnings;
use strict;


use lib qw(@PERLLIBDIR@);

use MotifUtils qw(seq_to_intern intern_to_meme read_background_file);

use Getopt::Long;
use Pod::Usage;

=head1 NAME

iupac2meme - Converts IUPAC motifs into MEME motifs.

=head1 SYNOPSIS

iupac2meme [options] <iupac motif>+

 Options: 
  -alpha DNA|PROTEIN            IUPAC alphabet; default: DNA
  -numseqs <numseqs>            assume frequencies based on this many 
                                sequences; default: 20
  -bg <background file>         file with background frequencies of letters; 
                                default: uniform background
  -pseudo <total pseudocounts>  add <total pseudocounts> times letter 
                                background to each frequency; default: 0
  -logodds                      output the log-odds (PSSM) and frequency 
                                (PSPM) motifs; default: PSPM motif only
  -url <website>                website for the motif; The motif name is 
                                substituted for MOTIF_NAME; default: no url
  -nosort			don't sort the order of motifs
 
 Converts IUPAC motifs into MEME motifs.
 
 Example IUPAC DNA motif: ACGGWNNYCGT
 Example IUPAC PROTEN motif: IKLVBZYXXHG

 Writes standard output.

=cut

# Set option defaults
my $alph_type = 'DNA';
my $num_seqs = 20;
my $bg_file;
my $pseudo_total = 0;
my $print_logodds = 0;
my $url_pattern = "";
my $no_sort = 0;
my @motif_strings = ();

GetOptions("alpha=s" => \$alph_type, "numseqs=i" => \$num_seqs, 
  "bg=s" => \$bg_file, "pseudo=f" => \$pseudo_total, "logodds" => \$print_logodds,
  "url=s" => \$url_pattern, "nosort" => \$no_sort) or pod2usage(2);
@motif_strings = @ARGV;

#check alpha type
$alph_type = uc($alph_type);
pod2usage("Option -alpha must be either DNA or PROTEIN.") if ($alph_type !~ m/(DNA|PROTEIN)/);
#check num seqs
pod2usage("Option -numseqs must have a positive value.") if ($num_seqs < 0);
#check pseudo total
pod2usage("Option -pseudo must have a positive value.") if ($pseudo_total < 0);
#check IUPAC motifs
pod2usage("At least one IUPAC motif must be specified.") if (!@motif_strings);

#sort the motifs
@motif_strings = sort(@motif_strings) unless $no_sort;

# get the background model
my %bg = &read_background_file($alph_type eq 'DNA', $bg_file);


#
# convert the IUPAC motifs to MEME format
#
my $num_motifs = 0;
foreach  my $iupac_motif (@motif_strings) {
  my $url = $url_pattern;
  $url =~ s/MOTIF_NAME/$iupac_motif/g;
  my ($motif, $errors) = seq_to_intern(\%bg, $iupac_motif, $num_seqs, $pseudo_total, url => $url);
  print STDERR join("\n", @{$errors}), "\n" if @{$errors};
  print intern_to_meme($motif, $print_logodds, 1, !($num_motifs++)) if $motif;
} # convert motif to MEME format