#!/usr/bin/env perl

use 5.28.0;
use warnings;
use autodie;

use Text::CSV;

use constant {
    SEP_CHAR => "\t",
    BED_CHR => 0,
    BED_START => 1,
    BED_END => 2,
    BED_STRAND => 5,
    BED_LINE => 6,
};

my (%start_plus, %start_minus, %start_dud);

my %dispatch = (
    '+' => sub { ++$start_plus{$_[BED_CHR]}{$_[BED_START]} },
    '-' => sub { ++$start_minus{$_[BED_CHR]}{$_[BED_END]} },
    '0' => sub { $start_dud{$_[BED_CHR]}{$_[BED_LINE]} = $_[BED_STRAND] },
);

my $csv = Text::CSV::->new({sep_char => SEP_CHAR});

while (my $row = $csv->getline(\*DATA)) {
    next if 0 == index $row->[0], '#';
    my $sign = exists $dispatch{$row->[BED_STRAND]} ? $row->[BED_STRAND] : 0;
    $dispatch{$sign}->(@$row, $.);
}

# This part for testing and demonstration purposes only
use Data::Dump;
say '=' x 10, ' Raw Extracted Data ', '=' x 20;
say 'Plus Strands';
say '-' x 50;
dd \%start_plus;
say '-' x 50;
say 'Minus Strands';
say '-' x 50;
dd \%start_minus;
say '-' x 50;
say 'Problem Strands';
say '-' x 50;
dd \%start_dud;
say '=' x 50;
# End this testing & demo part

my %filehandle_for;

for my $chr (sort keys %start_plus) {
    for my $file_id (ALL => $chr) {
        my $fh = _get_results_fh(\%filehandle_for, $file_id);
        $fh->say(join SEP_CHAR, CHR => 'Plus Strand BedGraph:');

        for my $key (sort {$a <=> $b} keys %{$start_plus{$chr}}) {
            $fh->say(join SEP_CHAR, $chr, $key + 1, $start_plus{$chr}{$key});
        }
    }
}

# This part for testing and demonstration purposes only
say "\n", '=' x 10, ' Output Files ', '=' x 26;
for my $outfile (qw{
    pm_11135183_bio_bed_modified_chr7_results.bed
    pm_11135183_bio_bed_modified_chr8_results.bed
    pm_11135183_bio_bed_modified_ALL_results.bed
}) {
    say $outfile;
    say '-' x 50;
    system cat => $outfile;
    say '-' x 50;
}
# End this testing & demo part

sub _get_results_fh {
    my ($fh_for, $chr) = @_;

    return $fh_for->{$chr} || _gen_results_fh($fh_for, $chr);
}

sub _gen_results_fh {
    my ($fh_for, $chr) = @_;

    my $fmt = 'pm_11135183_bio_bed_modified_%s_results.bed';
    my $filename = sprintf $fmt, $chr;
    open my $fh, '>', $filename;
    $fh_for->{$chr} = $fh;

    return $fh;
}

__DATA__
#chromosome start   end position    col-5   strand
chr7    127471196   127472363   Pos1    0   @
chr7    127471196   127472363   Pos1    0   +
chr7    127471196   127472363   Pos1    0   +
chr7    127471196   127472363   Pos1    0   +
chr7    127471196   127472363   Pos1    0   +
chr7    127471196   127472363   Pos1    0   +
chr7    127472363   127473530   Pos2    0   +
chr7    127473530   127474697   Pos3    0   -
chr7    127474697   127475864   Pos4    0   -
chr7    127474697   127475864   Pos4    0   _
chr8    40000   40500   Pos5    0   +
chr8    40000   40600   Pos5    0   +
chr8    40000   40650   Pos5    0   =
chr8    40000   40650   Pos5    0   +
chr8    41000   41200   Pos6    0   -

##</code><code>##

$ ./pm_11135183_bio_bed_modified.pl
========== Raw Extracted Data ====================
Plus Strands
--------------------------------------------------
{ chr7 => { 127471196 => 5, 127472363 => 1 }, chr8 => { 40000 => 3 } }
--------------------------------------------------
Minus Strands
--------------------------------------------------
{ chr7 => { 127474697 => 1, 127475864 => 1 }, chr8 => { 41200 => 1 } }
--------------------------------------------------
Problem Strands
--------------------------------------------------
{ chr7 => { 2 => "\@", 11 => "_" }, chr8 => { 14 => "=" } }
==================================================

========== Output Files ==========================
pm_11135183_bio_bed_modified_chr7_results.bed
--------------------------------------------------
CHR     Plus Strand BedGraph:
chr7    127471197       5
chr7    127472364       1
--------------------------------------------------
pm_11135183_bio_bed_modified_chr8_results.bed
--------------------------------------------------
CHR     Plus Strand BedGraph:
chr8    40001   3
--------------------------------------------------
pm_11135183_bio_bed_modified_ALL_results.bed
--------------------------------------------------
CHR     Plus Strand BedGraph:
chr7    127471197       5
chr7    127472364       1
CHR     Plus Strand BedGraph:
chr8    40001   3
--------------------------------------------------

##</code><code>##

{
    my %filehandle_for;

    sub _get_results_fh { my ($chr) = @_; ... }

    sub _gen_results_fh { my ($chr) = @_; ... }
}