package sRNAPipe::subgroups;

use strict;
use warnings;
use Exporter;
our @ISA = qw( Exporter );
our @EXPORT_OK = qw( &subgroups );

use POSIX;
use File::Copy;
use FindBin;
use lib "$FindBin::Bin/../lib";
use sRNAPipe::align qw ( get_hash_alignment );

sub subgroups
{
    my ($fin, $dir, $mis, $mis_TE, $proc, $tRNAs, $rRNAs, $snRNAs, $miRNAs, $transcripts, $TE, $min_si, $max_si, $min_pi, $max_pi, $report ) = @_;
    my (@files, $sum, $pie, $repar, %ismapped, %isjunk, %repartition, @junk_ref, @all_ref );

    srand();
    print $report "----------------------------\n";
    print $report "Create subgroups:\nfastq_in: $fin\ndirectory_out: $dir\nmismatches: $mis\nmismatches TE: $mis_TE\n";

    mkdir $dir;
    $dir = $dir.'/' unless $dir =~ /(.*)\/$/;

    my $accept_miRNas = $dir.'miRNAs.fastq';
    my $reject_miRNAs = $dir.'miRNAs_rejected.fastq';
    my $sam_miRNAs = $dir.'miRNAs.sam';
    my @tmp = get_hash_alignment($miRNAs, $mis, 1, 1, $accept_miRNas, $reject_miRNAs, $fin, $proc, 'miRNAs',$sam_miRNAs, $report);
    my $mi = $tmp[0]; my $sam = '';
    $repartition{'miRNAs'} = $mi;


    my $reject_rRNAs = $dir.'rRNAs_rejected.fastq';
    if ( $rRNAs eq 'None')
    {
        move($reject_miRNAs,$reject_rRNAs);
    }
    else
    {
        $sam = new String::Random;
        $sam = $sam->randpattern("CCcccccc");
        @tmp = get_hash_alignment($rRNAs, $mis, 0, 1, 'NA', $reject_rRNAs, $reject_miRNAs, $proc, 'rRNAs', $sam, $report);
        $repartition{'rRNAs'} = $tmp[0];
        unlink $sam, $sam.'_aln.err', $sam.'_samse.err';
    }

    my $reject_tRNAs = $dir.'rRNAs_rejected.fastq';
    if ( $rRNAs eq 'None')
    {
        move($reject_rRNAs,$reject_tRNAs);
    }
    else
    {
        $sam = new String::Random;
        $sam = $sam->randpattern("CCcccccc");
        @tmp = get_hash_alignment($tRNAs, $mis, 0, 1, 'NA', $reject_tRNAs, $reject_rRNAs, $proc, 'tRNAs', $sam, $report);
        $repartition{'tRNAs'} = $tmp[0];
        unlink $sam, $sam.'_aln.err', $sam.'_samse.err';
    }


    my $bonafide = $dir.'bonafide_reads.fastq';
    if ( $rRNAs eq 'None')
    {
        move($reject_tRNAs,$bonafide);
    }
    else
    {
        $sam = new String::Random;
        $sam = $sam->randpattern("CCcccccc");
        @tmp = get_hash_alignment($snRNAs, $mis, 0, 1, 'NA', $bonafide, $reject_tRNAs, $proc, 'snRNAs', $sam, $report);
        $repartition{'snRNAs'} = $tmp[0];

        unlink $sam, $sam.'_aln.err', $sam.'_samse.err';
    }
    my $bo = $tmp[1];

    my $sam_transcripts = $dir.'transcripts.sam';
    my $reject_transcripts = $dir.'rejected_transcripts.fastq';
    @tmp = get_hash_alignment($transcripts, $mis, 0, 1, 'NA', $reject_transcripts, $bonafide, $proc, 'transcripts', $sam_transcripts, $report, $dir.'transcripts.fai');
    $repartition{'transcripts'} = $tmp[0];

    
    my $sam_TEs = $dir.'TEs.sam';
    my $reject_TEs = $dir.'rejected.fastq';
    @tmp = get_hash_alignment($TE, $mis_TE, 0, 1, 'NA', $reject_TEs, $reject_transcripts, $proc, 'TEs', $sam_TEs, $report, $dir.'TEs.fai' );
    $repartition{'TEs'} = $tmp[0] ; $repartition{'others'} = $tmp[1];
    unlink $sam, $sam.'_aln.err', $sam.'_samse.err';
    unlink $reject_transcripts;
    unlink $reject_rRNAs;
    unlink $reject_miRNAs;
    unlink $reject_tRNAs;

    #create repartition
    my $pi = fastqSubgroups($bonafide, $dir, $min_si, $max_si, $min_pi, $max_pi );

    open (my $re, '>'.$dir.'repartition.txt') || die "cannot open $dir repartition.txt $!\n";
    print $re "type\tnumber\tpercentage\n";
    $sum += $_ foreach values %repartition;
    foreach my $k    ( sort keys    %repartition )
    {
        my $prct = 0;
        $prct = $repartition{$k} / $sum * 100 if $sum != 0;
        print $re "$k\t$repartition{$k}\t"; printf $re "%.2f\n",$prct;
    }
    return ( $bo, $mi, $pi);
}

sub fastqSubgroups
{
    my ( $fastq, $output_directory, $min_si, $max_si, $min_pi, $max_pi ) = @_;
    my $fastq_siRNA = $output_directory."siRNAs.fastq";
    my $fastq_piRNA = $output_directory."piRNAs.fastq";

    open my $fic, '<', $fastq || die "cannot open input file $! \n";
    open my $si, '>', $fastq_siRNA || die "cannot open siRNA.fastq $! \n";
    open my $pi, '>', $fastq_piRNA || die "cannot open piRNA.fastq $! \n";
    
    my ($length, $cmp, $type, $siRNA_number, $miRNA_h_number, $piRNA_number, $not_pi_number) = (0,0,0,0,0,0,0);
    my (@fastq) =(); my $seq_name;
    my $out;
    while(<$fic>)
    {
        chomp $_;
        $cmp++;
        if ($cmp == 1)
        {
            die "file do not contain a @ at line $cmp\n" unless ($_ =~ /^\@/ );
            $type = 0; @fastq = ();
            if ($_ =~ /^\@(.*)\s.*/) { $seq_name = $1;}
            elsif ($_ =~ /^\@(.*)/) {$seq_name = $1;}
            push(@fastq,$_);
        }
        elsif ($cmp == 2)
        {
            #die "unrecognized symbol at line $cmp\n" unless $_ =~ /[atcgATCGnN]+/;
            push(@fastq,$_);
            $length = length($_);
            $type = 0;
            if ( $length >= $min_si    && $length <= $max_si )
            {
                 $type = 2;
                 $siRNA_number++;
            }
            if ($length >= $min_pi    && $length <= $max_pi )
            {
                $type += 4;
                $piRNA_number++;
            }
        }
        elsif ($cmp == 3 )
        {
            die "file do not contain a + at line $cmp\n" unless $_ =~ /^\+/;
            push(@fastq,$_);
        }
        elsif ($cmp == 4 )
        {
            push(@fastq,$_);
            $cmp = 0;
            if ($type != 0)
            {
                if ($type & 4 ) { foreach my $t (@fastq) { print $pi $t."\n";} }
                if ($type & 2 ) { foreach my $t (@fastq) { print $si $t."\n";} }
            }
        }
    }
    close $fic;
    close $si; close $pi;
    return ($piRNA_number);
}

1;