push @sort_array, $trial_1;
      		push @pointer_array, $key_r;

##</code><code>##

               push @sort_array, [ $trial_1, $key_r ];

##</code><code>##

           my @sorted = sort{ $a->[ 0 ] <=> $b->[ 0 ] } @sort_array;

##</code><code>##

my( $closest, $pointer ) = @{ $sorted[ 0 ] };

##</code><code>##

#!/usr/bin/perl -slw
use strict;
use integer;
use vars qw( %tf1 %tf2 );

## Establish an array of all chromosome files.
my @files = ("chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9",
             "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17",
             "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY");

## Loop through each file, calculate the overlaps, and output to file.
foreach (@files) {
    print STDOUT scalar localtime;
    open TF1, "<", "TF1.$_.gff" or die "Cannot open the TF1 hit file!";  ## tf1 hit file
    open TF2, "<", "TF2.$_.gff" or die "Cannot open the TF2 hit file!"; ## tf2 hit file
    open OUT, ">", "both.$_.gff" or die "Cannot open the output file!";    ## output file
    
    while (<TF1>) {
        chomp;
        my ($location, undef, $type, $start, $end, $score, $strand, undef) = split "\t"; ## Parse
        my ($chr, $location_numbers) = split "_", $location;                                    ## Get the chromosome
        my ($target_start, $target_end) = split "-", $location_numbers; ## Get the start site for the 10kb sequence "blasted" against
        my $new_start = $target_start + $start;  ## Use this for true genomic location
        my $new_end = $target_start + $end;      ## Use thie for true genomic location
        
        ## Build a hash and put the data inside;
        $tf1{ $new_start }[0] = $chr;
        $tf1{ $new_start }[1] = $type; ## Transcription factor
        $tf1{ $new_start }[2] = $new_end;
        $tf1{ $new_start }[3] = $score; ## Alignment score from PWM blast
        $tf1{ $new_start }[4] = $strand; ## Strand where the match is found
    }
    
    while (<TF2>) {
        chomp;
        my ($location, undef, $type, $start, $end, $score, $strand, undef) = split "\t"; ## Parse
        my ($chr, $location_numbers) = split "_", $location;                                    ## Get the chromosome
        my ($target_start, $target_end) = split "-", $location_numbers; ## Get the start site for the 10kb sequence "blasted" against
        my $new_start = $target_start + $start;  ## Use this for true genomic location
        my $new_end = $target_start + $end;      ## Use thie for true genomic location
        
        ## Build a hash and put the data inside;
        $tf2{ $new_start }[0] = $chr;
        $tf2{ $new_start }[1] = $type; ## Transcription factor
        $tf2{ $new_start }[2] = $new_end;
        $tf2{ $new_start }[3] = $score; ## Alignment score from PWM blast
        $tf2{ $new_start }[4] = $strand; ## Strand where the match is found
    }
    
    ## Close the unused files
    close TF1;
    close TF2;
    
    OUTER:foreach my $key_c (sort keys %tf2) {
        my @sort_array = ();
	    my @pointer_array = ();
        my $start_c = $key_c;
        my $end_c = $tf2{ $key_c }[2];
        
        INNER:foreach my $key_r (sort keys %tf1) {
            my $start_r = $key_r;
            my $end_r = $tf1{ $key_r }[2];
            my $trial_1 = $start_r - $end_c;
            my $trial_2 = $start_c - $end_r;

            if ($trial_1 >= 0) {
                push @sort_array, $trial_1;
        		push @pointer_array, $key_r;
                next INNER;
            }
            elsif ($trial_2 >=0) {
                push @sort_array, $trial_2;
        		push @pointer_array, $key_r;
                next INNER;
            }
            else { next INNER; }
        }
        
        my @sorted_indexes = sort{ $sort_array[ $a ] <=> $sort_array[ $b ] } 0 .. $#sortedArray;
        
    	my $closest = $sort_array[ $sorted_indexes[ 0 ] ];
    	my $pointer = $pointer_array[ $sorted_indexes[ 0 ] ];

        if ($closest < 50) {
            print OUT join "\t", 
                $tf2{ $key_c }[0], $tf2{ $key_c }[1], 'tf2', $start_c, $end_c,
                $tf2{ $key_c }[3], $tf2{ $key_c }[4], 'tf1', $pointer,
                $tf1{ $pointer }[2], $tf1{ $pointer }[3], $tf1{ $pointer }[4];
        }
        else { next OUTER; }
    }

    ## Close the output file
    close OUT;
    print STDOUT scalar localtime;

} ## cycle through again til done with all files


##</code><code>##

#!/usr/bin/perl -slw
use strict;
use integer;
use vars qw( %tf1 %tf2 );

## Establish an array of all chromosome files.
my @files = ("chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9",
             "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17",
             "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY");

## Loop through each file, calculate the overlaps, and output to file.
foreach (@files) {
    print STDOUT scalar localtime;
    open TF1, "<", "TF1.$_.gff" or die "Cannot open the TF1 hit file!";  ## tf1 hit file
    open TF2, "<", "TF2.$_.gff" or die "Cannot open the TF2 hit file!"; ## tf2 hit file
    open OUT, ">", "both.$_.gff" or die "Cannot open the output file!";    ## output file
    
    while (<TF1>) {
        chomp;
        my ($location, undef, $type, $start, $end, $score, $strand, undef) = split "\t"; ## Parse
        my ($chr, $location_numbers) = split "_", $location;                                    ## Get the chromosome
        my ($target_start, $target_end) = split "-", $location_numbers; ## Get the start site for the 10kb sequence "blasted" against
        my $new_start = $target_start + $start;  ## Use this for true genomic location
        my $new_end = $target_start + $end;      ## Use thie for true genomic location
        
        ## Build a hash and put the data inside;
        $tf1{ $new_start }[0] = $chr;
        $tf1{ $new_start }[1] = $type; ## Transcription factor
        $tf1{ $new_start }[2] = $new_end;
        $tf1{ $new_start }[3] = $score; ## Alignment score from PWM blast
        $tf1{ $new_start }[4] = $strand; ## Strand where the match is found
    }
    
    while (<TF2>) {
        chomp;
        my ($location, undef, $type, $start, $end, $score, $strand, undef) = split "\t"; ## Parse
        my ($chr, $location_numbers) = split "_", $location;                                    ## Get the chromosome
        my ($target_start, $target_end) = split "-", $location_numbers; ## Get the start site for the 10kb sequence "blasted" against
        my $new_start = $target_start + $start;  ## Use this for true genomic location
        my $new_end = $target_start + $end;      ## Use thie for true genomic location
        
        ## Build a hash and put the data inside;
        $tf2{ $new_start }[0] = $chr;
        $tf2{ $new_start }[1] = $type; ## Transcription factor
        $tf2{ $new_start }[2] = $new_end;
        $tf2{ $new_start }[3] = $score; ## Alignment score from PWM blast
        $tf2{ $new_start }[4] = $strand; ## Strand where the match is found
    }
    
    ## Close the unused files
    close TF1;
    close TF2;
    
    foreach my $key_c ( keys %tf2 ) {
        my( $best, $best_key ) = ( 1e99, '' ); 
        my $start_c = $key_c;
        my $end_c = $tf2{ $key_c }[2];
        
        foreach my $key_r ( keys %tf1) {
            my $start_r = $key_r;
            my $end_r = $tf1{ $key_r }[2];
            my $trial_1 = $start_r - $end_c;
            my $trial_2 = $start_c - $end_r;

            if ($trial_1 >= 0) {
                if( $trial_1 < $best ) {
                    $best = $trial_1;
                    $best_key = $key_r;
                }
            }
            elsif ($trial_2 >=0) {
                if( $trial_2 < $best ) {
                    $best = $trial_2;
                    $best_key = $key_r;
                }
            }
        }

        if( $best < 50 ) {
            print OUT join "\t", 
                $tf2{ $key_c }[0], $tf2{ $key_c }[1], 'tf2', $start_c, $end_c,
                $tf2{ $key_c }[3], $tf2{ $key_c }[4], 'tf1', $best_key,
                $tf1{ $best_key}[2], $tf1{ $best_key}[3], $tf1{ $best_key}[4];
        }
    }

    ## Close the output file
    close OUT;
    print STDOUT scalar localtime;

} ## cycle through again til done with all files