--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bin/subgroups.pm	Wed Dec 13 10:40:50 2017 -0500
@@ -0,0 +1,149 @@
+package subgroups;
+
+use strict;
+use warnings;
+use Exporter;
+our @ISA = qw( Exporter );
+our @EXPORT_OK = qw( &subgroups );
+
+use POSIX;
+use FindBin;
+use lib $FindBin::Bin;
+use align qw ( get_hash_alignment );
+
+sub subgroups
+{
+	my ($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];
+	$repartition{'miRNAs'} = $mi;
+
+	my $sam = new String::Random;
+	$sam = $sam->randpattern("CCcccccc");
+	my $reject_rRNAs = $dir.'rRNAs_rejected.fastq';
+	@tmp = get_hash_alignment($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';
+
+	$sam = new String::Random;
+	$sam = $sam->randpattern("CCcccccc");
+	my $reject_tRNAs = $dir.'tRNAs_rejected.fastq';
+	@tmp = get_hash_alignment($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';
+
+	$sam = new String::Random;
+	$sam = $sam->randpattern("CCcccccc");
+	my $bonafide = $dir.'bonafide_reads.fastq';
+	@tmp = get_hash_alignment($snRNAs, $mis, 0, 1, 'NA', $bonafide, $reject_tRNAs, $proc, 'snRNAs', $sam, $report);
+	$repartition{'snRNAs'} = $tmp[0];
+	my $bo = $tmp[1];
+	unlink $sam, $sam.'_aln.err', $sam.'_samse.err';
+
+	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;