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

my $line;
my @array;
my $file;
my @files;
my $counter;
my $normalName;
my $yName;
my %type_normalName_cutoff_chromosome_positions;
my %type_normalName_cutoff_chromosomes;
my @chromosomes;
my @positions;
my $position;
my $chromosome;
my $type;
my $cutoff;
my $path;
my @types;
my %seen_type;
my @cutoffs;
my %seen_cutoff;
my %type_cliques;
my @cliques;
my $clique;
my %type_clique_normalNames;
my @normalNames;
my %type_clique_seen;
my %type_clique_cutoff_chromosomes;
my %type_clique_cutoff_chromosome_positions;
my %type_clique_cutoff_chromosome_position_seen;
my %type_clique_cutoff_chromosome_seen;
my %type_clique_cutoff_chromosome_position_count;
my %chromosome_add;
my $genomicPosition;
my %chromosome_length;
my $genomeLength;
my $outputFile;
my $count;
my $bin;
my $binSize;
my $highestBin;

$binSize = 20000;

$chromosome_length{1} = 230208;
$chromosome_length{2} = 813178;
$chromosome_length{3} = 316616;
$chromosome_length{4} = 1531916;
$chromosome_length{5} = 576869;
$chromosome_length{6} = 270148;
$chromosome_length{7} = 1090946;
$chromosome_length{8} = 562642;
$chromosome_length{9} = 439885;
$chromosome_length{10} = 745666;
$chromosome_length{11} = 666454;
$chromosome_length{12} = 1078174;
$chromosome_length{13} = 924429;
$chromosome_length{14} = 784331;
$chromosome_length{15} = 1091287;
$chromosome_length{16} = 948062;

$chromosome_add{1} = 0;
$chromosome = 2;
while ($chromosome <= 16) {
    $chromosome_add{$chromosome} = $chromosome_add{$chromosome - 1} + $chromosome_length{$chromosome - 1};
    $chromosome++;
}

$genomeLength = 0;

$chromosome = 1;
while ($chromosome <= 16) {
    $genomeLength += $chromosome_length{$chromosome};
    $chromosome++;
}

print "the length of the entire genome is $genomeLength\n";
$highestBin = (int(($genomeLength - 1)/$binSize)) + 1;
print "the highest bin number is $highestBin\n";


$path = "/Users/eric/post_disaster_mass_spec/consolidate_results/";

opendir (DIR, "$path");
@array = readdir DIR;
closedir DIR;

foreach $file (@array) {
    if ($file =~ /^gold_standard_\S+051809_1\.txt$/) {
        #print "$file\n";
        $file = "$path"."$file";
        push (@files, $file);
    }
}

foreach $file (@files) {
    if ($file =~ /gold_standard_(\S+)_cutoff0p0(\d)_051809_1\.txt$/) {
        $type = $1;
        $cutoff = $2;
        #if ($type eq "peptide") {
        #    $type = "protein";
        #}
        unless ($seen_type{$type}) {
            push (@types, $type);
            $seen_type{$type} = 1;
        }
        unless ($seen_cutoff{$cutoff}) {
            push (@cutoffs, $cutoff);
            $seen_cutoff{$cutoff} = 1;
        }
    }
    else {
        die "unexpected file name: $file\n";
    }
    open (INPUT, "<$file") or die "can't find $file\n";
    while ($line = <INPUT>) {
        chomp $line;
        if ($line =~ /\r/) {
            die "possible new line problem\n";
        }
        if ($line =~ /\S/) {
            @array = split /\t/, $line;
            unless ($#array == 28) {
                die "problem splitting this line into 29 elements ($#array):\n$line\n";
            }
            if ($line =~ /^type_of_measurement\t/) {
                print "$array[0]\t$array[2]\t$array[5]\t$array[6]\n";
            }
            else {
                $type = $array[0];
                $normalName = $array[2];
                $chromosome = $array[5];
                $position = $array[6];
                push (@{ $type_normalName_cutoff_chromosome_positions{$type}{$normalName}{$cutoff}{$chromosome} }, $position);
                push (@{ $type_normalName_cutoff_chromosomes{$type}{$normalName}{$cutoff} }, $chromosome);
            }
        }
    }
    close INPUT;
}

@types = sort { lc($a) cmp lc($b) } @types;
@cutoffs = sort { $a <=> $b } @cutoffs;

@array = ();
@files = ();

$path = "./";

opendir (DIR, "$path");
@array = readdir DIR;
closedir DIR;

foreach $file (@array) {
    if ($file =~ /^complete_graphs_(\S+)s_070309_3\.txt$/) {
        print "$file\n";
        push (@files, $file);
    }
}

foreach $file (@files) {
    if ($file =~ /^complete_graphs_(\S+)s_070309_3\.txt$/) {
        #$type = $1;
    }
    else {
        die "unexpected file name: $file\n";
    }
    open (INPUT, "<$file") or die "can't find $file\n";
    while ($line = <INPUT>) {
        chomp $line;
        if ($line =~ /\r/) {
            die "possible new line problem\n";
        }
        if ($line =~ /\S/) {
            @array = split /\t/, $line;
            unless ($#array == 6) {
                die "problem splitting this line into 7 elements ($#array):\n$line\n";
            }
            if ($line =~ /^type_of_measurement\t/) {
                print "$array[0]\t$array[1]\t$array[4]\n";
            }
            else {
                $type = $array[0];
                $clique = $array[1];
                $normalName = $array[4];
                unless ($type_clique_seen{$type}{$clique}) {
                    push (@{ $type_cliques{$type} }, $clique);
                    $type_clique_seen{$type}{$clique} = 1;
                }
                foreach $cutoff (@cutoffs) {
                    #type_normalName_cutoff_chromosome_positions
                    if ($type_normalName_cutoff_chromosomes{$type}{$normalName}{$cutoff}) {
                        @chromosomes = @{ $type_normalName_cutoff_chromosomes{$type}{$normalName}{$cutoff} };
                        @chromosomes = sort { $a <=> $b } @chromosomes;
                        foreach $chromosome (@chromosomes) {
                            unless ($type_clique_cutoff_chromosome_seen{$type}{$clique}{$chromosome}) {
                                push (@{ $type_clique_cutoff_chromosome_seen{$type}{$clique}{$chromosome} }, $chromosome);
                                $type_clique_cutoff_chromosome_seen{$type}{$clique}{$chromosome} = 1;
                            }
                            @positions = @{ $type_normalName_cutoff_chromosome_positions{$type}{$normalName}{$cutoff}{$chromosome} };
                            @positions = sort { $a <=> $b } @positions;
                            foreach $position (@positions) {
                                unless ($type_clique_cutoff_chromosome_position_seen{$type}{$clique}{$cutoff}{$chromosome}{$position}) {
                                    push (@{ $type_clique_cutoff_chromosome_positions{$type}{$clique}{$cutoff}{$chromosome}{$position} }, $position);
                                    $type_clique_cutoff_chromosome_position_seen{$type}{$clique}{$cutoff}{$chromosome}{$position} = 1;
                                }
                                $type_clique_cutoff_chromosome_position_count{$type}{$clique}{$cutoff}{$chromosome}{$position}++;
                            }
                        }
                    }
                    else {
                        
                    }
                }
            }
        }
    }
    close INPUT;
}

open (OUTPUT1, ">cliques_mapped_bin_counts_072109_1.txt");
open (OUTPUT2, ">cliques_mapped_bin_counts_072109_1.xls");

print OUTPUT1 "type_of_measurement\tclique\tcutoff_percent\tchromosome\tposition\tgenomic_position\t$binSize"."_bin\thighest_position\thighest_bin_number_starting_with_bin_number_1\n";
print OUTPUT2 "type_of_measurement\tclique\tcutoff_percent\tchromosome\tposition\tgenomic_position\t$binSize"."_bin\thighest_position\thighest_bin_number_starting_with_bin_number_1\n";

foreach $type (@types) {
    @cliques = @{ $type_cliques{$type} };
    @cliques = sort { $a <=> $b } @cliques;
    foreach $clique (@cliques) {
        foreach $cutoff (@cutoffs) {
            if ($type_clique_cutoff_chromosomes{$type}{$clique}{$cutoff}) {
                @chromosomes = @{ $type_clique_cutoff_chromosomes{$type}{$clique}{$cutoff} };
                @chromosomes = sort { $a <=> $b } @chromosomes;
                foreach $chromosome (@chromosomes) {
                    @positions = @{ $type_clique_cutoff_chromosome_positions{$type}{$clique}{$chromosome} };
                    @positions = sort { $a <=> $b } @positions;
                    foreach $position (@positions) {
                        $genomicPosition = $position + $chromosome_add{$chromosome};
                        $count = $type_clique_cutoff_chromosome_position_count{$type}{$clique}{$cutoff}{$chromosome}{$position};
                        $bin = (int(($genomicPosition - 1)/$binSize)) + 1;
                        print OUTPUT1 "$type\t$clique\t$cutoff\t$chromosome\t$position\t$genomicPosition\t$bin\t$genomeLength\t$highestBin\n";
                        print OUTPUT2 "$type\t$clique\t$cutoff\t$chromosome\t$position\t$genomicPosition\t$bin\t$genomeLength\t$highestBin\n";
                    }
                }
            }
        }
    }
}

close OUTPUT1;
close OUTPUT2;

print "done!\n";