#!/usr/bin/perl -w
use strict;

our (@window, @probe)=();

our @main = &open_file_main();
our @annot = &open_file_annot();
&outfile;

# loop through the main data file
OLC: foreach my $md (@main) {
    # remove newlines
    chomp $md; 
    # pull out chromosome #, window start, end
    my ($main_chrom, $winl, $winr) = split(/\t/, $md);
    # put the window start, end into array for further processing
    @window = ($winl, $winr);
    # loop through the "annotation" file
    ILC: foreach my $ad (@annot) {
        # pull out the chromosome #, window start, end
        my ($an_chrom, undef, undef, $prol, $pror, undef, undef, undef, $mess) = split(/\t/, $ad);
        # make sure the chromosomes match to save processor time, skip if no match
         if ($main_chrom ne $an_chrom) {next ILC;}
         # get the gene name fromt the $mess variable
        my (undef, undef, $name) = split(/\;/, $mess);
        # load the window start sites for the individual probes
        @probe = ($prol, $pror);
        # call the range_finding sub to look for matches
        my $return = range_find();
         if ($return eq 1) {
            # upon matching, print out the name of the gene along with the original values
            # and 
            print OUTPUT "$name\t $md\n";
            next OLC;
         }
         else {next ILC;}
    }
}

close OUTPUT;
exit;

sub open_file_main { # open the file, pull in the data
    print " What is the name of the ChIPOTle file\?";
    chomp (my $file = <STDIN>);
    open (FILE, $file) || die "Cannot open $!";
    my @data = <FILE>;
    close FILE;
    return @data;
}

sub open_file_annot { # open the file, pull in the data
    print " What is the name of the annotation file\?";
    chomp (my $file = <STDIN>);
    open (FILE, $file) || die "Cannot open $!";
    my @data = <FILE>;
    close FILE;
    return @data;
}

sub outfile { # open the outputfile
    open (OUTPUT, ">output.txt")|| die "Cannot open $!";
}

sub calc_range { # simple sub to create the full window from the start and end sites
    my @peaks = @_;
    my @peak_range = ($peaks[0] .. $peaks[1]);
    return @peak_range;
}

sub range_find { # loop in loop to look for ANY overlap of the values; will be a true/false return
    my @range1 = &calc_range(@window);
    my @range2 = &calc_range(@probe);
    my $test = pop @range2;
    my $test2 = pop @range1;
    OLC2: foreach my $value1 (@range1) {
        # look to see if the windows don't overlap 
        if ($test lt $window[0]) {return 0;}
        # look to see if the windows don't overlap
        elsif ($test2 lt $probe[0]) {return 0;}
        ILC2: foreach my $value2 (@range2) {
            if ( $value1 eq $value2) {return 1;}
            else {next ILC2;}
        }
    }
    return 0;
}

##</code><code>##

chr10	726178	726428	1.121753867297440e-012	1.160706397628387e-015	6	4.81000
chr10	4922028	4922428	2.163402534569952e-012	7.067018499345696e-014	9	4.43000
chr10	5126478	5127178	8.348017333255820e-013	8.243249541245406e-021	15	4.42000
chr10	14649778	14650028	2.090598548899472e-013	6.000728326245207e-018	6	5.04000
chr10	14651328	14651428	2.915017653920210e-012	1.890051416361198e-014	3	4.20000

##</code><code>##

chr1	NGS	primary_transcript	4224	7502	-1	-	.	ID=00003; accession=BC063682; Name=FLJ25222; ncbi_gene_id=374666; synonyms=-; description=CXYorf1-related protein; url=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db%3Dnucleotide%26cmd%3Dsearch%26term%3DBC063682
chr1	NGS	transcription_start_site	7502	7502	-1	-	.	Parent=00003; accession=BC063682; Name=FLJ25222; ncbi_gene_id=374666; synonyms=-; description=CXYorf1-related protein
chr1	NGS	primary_transcript	4268	7438	-2	-	.	ID=00005; accession=BC073913; Name=MGC52000; ncbi_gene_id=375260; synonyms=CXYorf1|MGC104889|MGC111476|MGC117230|MGC90409; description=CXYorf1-related protein; url=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db%3Dnucleotide%26cmd%3Dsearch%26term%3DBC073913
chr1	NGS	transcription_start_site	7438	7438	-2	-	.	Parent=00005; accession=BC073913; Name=MGC52000; ncbi_gene_id=375260; synonyms=CXYorf1|MGC104889|MGC111476|MGC117230|MGC90409; description=CXYorf1-related protein
chr1	NGS	primary_transcript	4268	14754	-3	-	.	ID=00004; accession=BC048328; Name=MGC52000; ncbi_gene_id=375260; synonyms=CXYorf1|MGC104889|MGC111476|MGC117230|MGC90409; description=CXYorf1-related protein; url=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db%3Dnucleotide%26cmd%3Dsearch%26term%3DBC048328
chr1	NGS	transcription_start_site	14754	14754	-3	-	.	Parent=00004; accession=BC048328; Name=MGC52000; ncbi_gene_id=375260; synonyms=CXYorf1|MGC104889|MGC111476|MGC117230|MGC90409; description=CXYorf1-related protein
chr1	NGS	primary_transcript	4268	19697	-4	-	.	ID=00006; accession=BC110996; Name=MGC52000; ncbi_gene_id=375260; synonyms=CXYorf1|MGC104889|MGC111476|MGC117230|MGC90409; description=CXYorf1-related protein; url=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db%3Dnucleotide%26cmd%3Dsearch%26term%3DBC110996