#!/usr/bin/perl -w

use strict;
use warnings;
use Getopt::Std;
use IO::File;
use File::Spec;

my %opts = ();
getopts('s:h', \%opts);

if (exists $opts{'h'}) {
    usage();
    exit 1;
}

#my $score_file = $ARGV[0] || '';

# Takes the score file from matrix_comparison.pl as input
my $score_file = $opts{'s'};

my $score_fh = IO::File->new("<$score_file")
      or die("can't open $score_file!\n$!");

#open( IN, $score_file ) or die "Can't open '$score_file'";

my $motif;
while ( defined( my $score_line = $score_fh->getline() ) ) {
    chomp $score_line;

    my $number;
    my $score;

    if ( $score_line =~ /^(MOTIF_\d+)/ ) {
        $motif = $1;
        next;
    } else {
#        ( $number, $score ) = split( /\s+/, $score_line );
        ( $number, $score ) = split( /\b\s/, $score_line );
    }

    if ( !( defined $motif && defined $number && defined $score ) ) {
        die "Wierdness!";
    }

    my $motif_path = sprintf "%d/%s", $number, $motif;
#    open( F, $motif_path ) or die "Can't open '$motif_path'";
    my $motif_path_fh = IO::File->new("<$motif_path")
	  or die("can't open $motif_path!\n$!");

    my $less_count = 0;
    my $tot_count  = 0;
#    while ( my $perm_line = <F> ) {
    while ( defined( my $perm_line = $motif_path_fh->getline() ) ) {
        chomp $perm_line;

        ++$tot_count;
        ++$less_count if ( $perm_line < $score );
    }
    $motif_path_fh->close();
#    close(F);

    my $summary_file = $motif . '_hits.list';

    open( MOTIF, ">>$summary_file" ) or die( "No summary!" );
    printf MOTIF "%s\t%.4f\t%4d\t%.3f\n",
	$motif_path, $score, $less_count,
	$less_count / $tot_count;
    close(MOTIF);
}

$score_fh->close();
#close(IN);

# Usage
sub usage
{
    print STDERR <<EOT;
permutation.pl version 1.0
Amonida Zadissa. 2006 (AgResearch, Otago University)

Calculates the statistical significance of the dissimilarity
scores from the matrix_comparison.pl programme.

Writes one file for each motif with the corresponding
information.

Usage:

\t$0
\t  -s file_for_statistics
\t$0 -h

EOT
}