--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bin/ppp.pm	Wed Dec 13 10:40:50 2017 -0500
@@ -0,0 +1,230 @@
+package ppp;
+
+use strict;
+use warnings;
+use FindBin;
+use lib $FindBin::Bin;
+use Rcall qw ( histogram );
+use Math::CDF;
+
+use Exporter;
+our @ISA = qw( Exporter );
+our @EXPORT_OK = qw( &ping_pong_partners );
+
+sub ping_pong_partners
+{
+  my ( $TE_fai, $sam, $dir, $max ) = @_;
+  my ( $hashRef, $dupRef, $hasPpp ) = count_mapped ( $TE_fai, $sam );
+  my ( %num_per_overlap_size, $overlap_number, $reverseR, $begRev, $endRev, $sensR, $begSens, $endSens, $snum, $rnum, $overlap );
+  my ( $SP, $AP, $SN, $AN, $txt );
+  my $flag = 0;
+  my @distri_overlap = (); my @overlaps_names = ();
+
+  open my $ppp_f, '>', $dir."ppp.txt" || die "cannot create ppp.txt $!\n";
+  foreach my $k ( sort keys %{$hashRef} )
+  {
+    my $v = $hashRef->{$k};
+    my $TE_dir = $dir.$k.'/';
+
+    %num_per_overlap_size = (); $overlap_number = 0;
+    $flag = 0;
+    for ( my $i = 0; $i <= $#{$v->[1]} ; $i++ )
+    {
+      $reverseR = ${$v->[1]}[$i] ;
+      $begRev = $reverseR->[0];
+      $endRev = $begRev + length($reverseR->[1]) - 1;
+
+      my $revR = reverse($reverseR->[1]);
+      $revR =~ tr/atgcuATGCU/tacgaTACGA/;
+
+      for ( my $j = 0; $j <= $#{$v->[0]}; $j++ )
+      {
+        $sensR = ${$v->[0]}[$j];
+        $begSens = $sensR->[0];
+        $endSens = $begSens + length($sensR->[1]) - 1;
+
+        if ( $begSens <= $endRev && $endSens > $endRev )
+        {
+          $flag = 1;
+          mkdir $TE_dir;
+          open  $txt, '>', $TE_dir.'overlap_size.txt' || die "cannot open repartition\n";
+
+          $overlap = $endRev - $begSens + 1;
+          $snum =  $dupRef->{$sensR->[0].$sensR->[1].$sensR->[2].$sensR->[3]};
+          $rnum = $dupRef->{$reverseR->[0].$reverseR->[1].$reverseR->[2].$reverseR->[3]};
+
+          if ( $overlap == 10 )
+          {
+            $hasPpp->{ $sensR->[0].$sensR->[1].$sensR->[2].$sensR->[3] } = 1;
+            $hasPpp->{ $reverseR->[0].$reverseR->[1].$reverseR->[2].$reverseR->[3] } = 1;
+          }
+          next if $overlap > $max;
+          if ( $snum < $rnum )
+          {
+            $num_per_overlap_size{$overlap} += $snum;
+            $overlap_number += $snum;
+          }
+          else
+          {
+            $num_per_overlap_size{$overlap} += $rnum ;
+            $overlap_number += $rnum ;
+          }
+        }
+      }
+    }
+    if ( $max != 0 )
+    {
+      my @overlaps = ();
+      push @overlaps_names, $k;
+      for my $i (1..$max)
+      {
+        $num_per_overlap_size{$i} = 0 unless exists( $num_per_overlap_size{$i} );
+        push @overlaps, $num_per_overlap_size{$i};
+      }
+      push @distri_overlap, \@overlaps;
+    }
+
+    if ( $flag == 1 )
+    {
+      open  $AP, '>', $TE_dir."antisensPPP.txt" || die "cannot create antisensPPP\n";
+      open  $AN, '>', $TE_dir."antisens.txt"  || die "cannot create antisens\n";
+      for ( my $i = 0; $i <= $#{$v->[1]} ; $i++ )
+      {
+        $reverseR = ${$v->[1]}[$i] ;
+        my $revR = reverse($reverseR->[1]);
+        $revR =~ tr/atgcuATGCU/tacgaTACGA/;
+        $rnum = $dupRef->{$reverseR->[0].$reverseR->[1].$reverseR->[2].$reverseR->[3]};
+        if ( $hasPpp->{ $reverseR->[0].$reverseR->[1].$reverseR->[2].$reverseR->[3] } == 1 )
+        {
+          print $AP ">$reverseR->[0]|$reverseR->[2]|$reverseR->[3]|$rnum\n$revR\n";
+        }
+        else
+        {
+          print $AN ">$reverseR->[0]|$reverseR->[2]|$reverseR->[3]|$rnum\n$revR\n";
+        }
+      }
+      close $AP; close $AN;
+
+      open  $SP, '>', $TE_dir."sensPPP.txt" || die "cannot create sensPPP\n";
+      open  $SN, '>', $TE_dir."sens.txt"  || die "cannot create sens\n";
+      for ( my $j = 0; $j <= $#{$v->[0]}; $j++ )
+      {
+        $sensR = ${$v->[0]}[$j];
+        $snum =  $dupRef->{$sensR->[0].$sensR->[1].$sensR->[2].$sensR->[3]};
+        if ( $hasPpp->{ $sensR->[0].$sensR->[1].$sensR->[2].$sensR->[3] } == 1 )
+        {
+          print $SP ">$sensR->[0]|$sensR->[2]|$sensR->[3]|$snum\n$sensR->[1]\n";
+        }
+        else
+        {
+          print $SN ">$sensR->[0]|$sensR->[2]|$sensR->[3]|$snum\n$sensR->[1]\n";
+        }
+      }
+      close $SP; close $SN;
+
+      my $histo_png = $TE_dir.'histogram.png';
+      histogram( \%num_per_overlap_size, $histo_png, $overlap_number );
+      print $txt "size\tnumber\tpercentage of the total overlap number\n";
+      foreach my $k ( sort {$a <=> $b} keys %num_per_overlap_size )
+      {
+        my $percentage = 0;
+        $percentage = $num_per_overlap_size{$k} * 100 / $overlap_number unless $overlap_number == 0;
+        print $txt "$k\t$num_per_overlap_size{$k}\t"; printf $txt "%.2f\n",$percentage;
+      }
+      close $txt;
+    }
+  }
+
+  foreach my $tabP (  @distri_overlap )
+  {
+    my $sum = sum($tabP);
+    my $ten = $tabP->[9];
+    my $mean = mean($tabP);
+    my $std = standard_deviation($tabP, $mean);
+    my $zsc = z_significance($ten, $mean, $std);
+    my $name = shift @overlaps_names;
+    my $prob = 'NA';
+    $prob =  1 - &Math::CDF::pnorm( $zsc ) if $zsc ne 'NA';
+    print $ppp_f (join ("\t", $name, $sum, $ten, $mean, $std, $zsc, $prob ),"\n" );
+  }
+  close $ppp_f;
+}
+
+sub count_mapped
+{
+  my ( $fai, $in_file ) = @_;
+  my ( %mapped, %dup, %has_ppp );
+
+  open my $f, '<', $fai || die "cannot open $fai $! \n";
+  while(<$f>)
+  {
+    if ($_ =~ /(.*)\t(\d+)\n/)
+    {
+      $mapped{$1} = [];
+      $mapped{$1}->[0] = []; $mapped{$1}->[1] = [];
+    }
+  }
+  close $f;
+
+  open my $infile, "samtools view  $in_file |"|| die "cannot open input file $! \n";
+  while(<$infile>)
+  {
+    unless ($_ =~ /^\@[A-Za-z][A-Za-z](\t[A-Za-z][A-Za-z0-9]:[ -~]+)+$/ || $_ =~ /^\@CO\t.*/ )
+    {
+      my @line = split (/\t/,$_);
+      if ($line[1] == 0)
+      {
+        unless ( exists ($dup{$line[3].$line[9].$line[1].$line[2]}) )
+        {
+          push @{$mapped{$line[2]}->[0]} , [$line[3], $line[9], $line[1],  $line[2]];
+          $has_ppp {$line[3].$line[9].$line[1].$line[2]} = 0;
+        }
+        $dup{$line[3].$line[9].$line[1].$line[2]}+=1;
+      }
+      elsif ($line[1] == 16)
+      {
+        unless ( exists ($dup{$line[3].$line[9].$line[1].$line[2]}) )
+        {
+          push @{$mapped{$line[2]}->[1]} , [$line[3], $line[9], $line[1],  $line[2]];
+          $has_ppp{$line[3].$line[9].$line[1].$line[2]} = 0;
+        }
+        $dup{$line[3].$line[9].$line[1].$line[2]}+=1
+      }
+    }
+  }
+  close $infile;
+  return (\%mapped, \%dup, \%has_ppp );
+}
+
+sub sum
+{
+  my $arrayref = shift;
+  my $result = 0;
+  foreach (@$arrayref) {$result += $_}
+  return $result;
+}
+
+sub mean
+{
+  my $arrayref = shift;
+  my $result;
+  foreach (@$arrayref) {$result += $_}
+  return $result / scalar(@$arrayref);
+}
+
+sub standard_deviation
+{
+  my ($arrayref, $mean) =  @_;
+  return sqrt ( mean ( [map $_**2 , @$arrayref ]) - ($mean**2));
+}
+
+sub z_significance
+{
+  my ($ten, $mean, $std) = @_;
+  my $z = 'NA';
+  $z = (($ten - $mean) / $std) if $std != 0;
+  return $z;
+}
+
+1;
+