#!/usr/bin/perl -w
#
# FILE: chen2meme
# AUTHOR: Timothy L. Bailey
# CREATE DATE: 18/12/2009
# DESCRIPTION: Convert a file containing list of TFBS motif matrices from 
# CHEN to MEME output format. 

use warnings;
use strict;

use lib qw(/mit/meme_v4.11.4/lib/perl);

use Alphabet qw(dna);
use MotifUtils qw(matrix_to_intern intern_to_meme read_background_file);

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

=head1 NAME

chen2meme - Converts a CHEN (concatenated) matrix file into MEME motifs.

=head1 SYNOPSIS

chen2meme [options]

 Options: 
  -skip <ID>                    skip this ID (may be repeated)
  -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                      print log-odds matrix, too; 
                                default: print frequency matrix only
  -url <website>                website for the motif; The motif name
                                is substituted for MOTIF_NAME;
  -h                            print usage message

 Converts a CHEN (concatenated) matrix file into MEME motifs.

 Reads standard input.
 Writes standard output.

=cut

# constants
my $sites = 10;

# Set option defaults
my %skips;
my $bg_file;
my $pseudo_total = 0;
my $print_logodds = 0;
my $url_pattern = "";
my $use_descr_as_name = 0;
my $help = 0;

# duplicates
my %dup_check = ();

GetOptions("skip=s" => sub {$skips{$_[1]} = 1}, "bg=s" => \$bg_file, 
  "pseudo=f" => \$pseudo_total, "logodds" => \$print_logodds, 
  "url=s" => \$url_pattern, "id" => \$use_descr_as_name, "h" => \$help) or pod2usage(2);
#check pseudo total
pod2usage("Option -pseudo must have a positive value.") if ($pseudo_total < 0);
#output help if requested
pod2usage(1) if $help;

# Get the background model.
my %bg = &read_background_file(&dna(), $bg_file);

# Read the input file.
my $num_skipped = 0;
my $num_motifs = 0;
my (%motifs, $motif_alt, $motif_name, $motif_matrix);
while (<>) {
  chomp;
  # skip blank lines
  next if (/^\s*$/);

  if (/^>(\S+)/) {
    my $next_name = $1;
    my @fields = split;
    my $next_alt = ($#fields > 0) ? $fields[1] : "";
    # create previous motif
    conditional_motif_output();
    # motif id line
    $motif_name = $next_name;
    $motif_alt = $next_alt;
    $motif_matrix = "";
  } else {
    $motif_matrix .= $_ . "\n";
  }

}

# create last motif
conditional_motif_output();

foreach my $name (sort keys %motifs) {
  print intern_to_meme($motifs{$name}, $print_logodds, 1, !($num_motifs++));
}

print(STDERR "Converted $num_motifs motifs.\n");
print(STDERR "Skipped $num_skipped motifs.\n");

1;


sub conditional_motif_output {
  if ($motif_matrix) {
    if (defined($skips{$motif_name})) {
      $num_skipped++;
    } else {
      my $url = $url_pattern;
      $url =~ s/MOTIF_NAME/$motif_name/g;
      # check for duplicate motif names
      if ($dup_check{$motif_name}) {
        my $seen = $dup_check{$motif_name};
        while ($dup_check{$motif_name . "_" . ($seen + 1)}) {
          $seen++;
        }
        $dup_check{$motif_name} = $seen + 1;
        $motif_name .= "_" . ($seen + 1);
      }
      $dup_check{$motif_name} = 1;

      my ($motif, $errors) = matrix_to_intern(\%bg, $motif_matrix, 'row', 
        $sites, $pseudo_total, id => $motif_name, alt => $motif_alt, url => $url);
      print(STDERR join("\n", @{$errors}), "\n") if @{$errors};
      $motifs{$motif_name} = $motif if $motif;
    }
  }
}