--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bin/align.pm	Wed Dec 13 10:40:50 2017 -0500
@@ -0,0 +1,457 @@
+package align;
+
+use strict;
+use warnings;
+use File::Basename;
+use String::Random;
+
+use FindBin;
+use lib $FindBin::Bin;
+use Rcall qw ( histogram );
+
+use Exporter;
+our @ISA     = qw( Exporter );
+our @EXPORT  = qw( &BWA_call &to_build &get_unique &sam_sorted_bam &get_hash_alignment &sam_to_bam_bg &sam_count &sam_count_mis &rpms_rpkm &get_fastq_seq &extract_sam );
+
+sub to_build
+{
+  my ( $toBuildTabP, $log, $newdir ) = @_;
+
+  foreach my  $pairs ( @{ $toBuildTabP } ) 
+  {
+    if (  $pairs->[0] == 1 ) 
+    {   
+      my $sym = $newdir.basename(${$pairs->[1]}).'_symlink.fa';
+      symlink( ${$pairs->[1]}, $sym );
+      ${$pairs->[1]} = $sym;
+      build_index ( ${$pairs->[1]}, $log );
+    }   
+  }
+}
+
+sub build_index
+{
+	my $to_index = shift;
+	my $log = shift;
+	my $index_log = $to_index.'_index.err';
+	`bwa index $to_index 2> $index_log`;
+	print $log "Creating index for $to_index\n";
+}
+
+sub get_unique
+{
+	my ( $sam, $s_uni, $out_prefix, $col_prefix, $details, $report ) = @_;
+
+	my $fout = $col_prefix.'_all_mappers.fastq'; 
+	my $funi = $col_prefix.'_unique_mappers.fastq';
+	my $frej = $col_prefix.'_unmapped.fastq';
+	
+  my $repartition = $out_prefix.'distribution.txt';
+	my $png_rep = $out_prefix.'distribution.png';
+	my ( %duplicates, %genome_hits) ;
+
+	#alignement to the first reference
+	my @return = sam_parse( $sam, $fout, $funi, $frej, $s_uni, \%duplicates, \%genome_hits, $report );
+	my $ref_fai = $return[4];
+	my $mappers =  $return[5];
+	my $mappers_uni = $return[6];
+	my $size_mappedHashR = $return[7];
+
+	if ( $details == 1 )
+	{
+		#print number of duplicates and hits number
+		my ($pourcentage, $total) =(0,0);
+
+		$total += $_ foreach values %{$size_mappedHashR};
+		open (my $rep, '>'.$repartition) || die "cannot create $repartition $!\n";
+		print $rep "size\tnumber\tpercentage\n";
+		foreach my $k (sort{$a cmp $b} keys (%{$size_mappedHashR}))
+		{
+			$pourcentage = 0;
+			$pourcentage = $size_mappedHashR->{$k} / $total * 100 unless $total ==0;
+
+			print $rep "$k\t$size_mappedHashR->{$k}\t";
+			printf $rep "%.2f\n",$pourcentage;
+		}
+
+		histogram($size_mappedHashR, $png_rep, $total);
+
+
+		my $dup = $out_prefix.'dup_mapnum.txt';
+		my $dup_u = $out_prefix .'dup_unique.txt';
+		my $dup_r = $out_prefix .'dup_nonmapp.txt';
+		open(my $tab,">".$dup) || die "cannot open output txt file\n";
+		open(my $tab_r,">".$dup_r) || die "cannot open output txt file\n";
+		open(my $tab_u,">".$dup_u) || die "cannot open output txt file\n";
+		print $tab "sequence\tcount\tmapnum\n";
+		print $tab_u "sequence\tcount\n";
+		print $tab_r "sequence\tcount\n";
+		foreach my $k (sort {$duplicates{$b} <=> $duplicates{$a}}keys %duplicates)
+		{
+			$duplicates{$k} = 0 unless exists($duplicates{$k});
+			$genome_hits{$k} = 0 unless exists($genome_hits{$k});
+			if ($genome_hits{$k} != 0) { print $tab $k."\t".$duplicates{$k}."\t".$genome_hits{$k}."\n"; }
+			else {print $tab_r $k."\t".$duplicates{$k}."\n";}
+			if ($genome_hits{$k} == 1) { print $tab_u $k."\t".$duplicates{$k}."\n"; }
+		}
+	close $dup; close $dup_r; close $dup_u;
+	}
+	return ( $ref_fai, $mappers, $mappers_uni );
+}
+
+sub sam_parse
+{
+	my ( $sam, $fastq_accepted, $fastq_accepted_unique, $fastq_rejected, $sam_unique, $duplicate_hashR, $best_hit_number_hashR, $report ) = @_ ;
+	my ($reads, $mappers, $mappersUnique, @garbage, %size_num, %size_num_spe, %number, %numberSens, %numberReverse, %unique_number, %numberNM, %numberM, %size);
+	$mappers = $mappersUnique = $reads = 0;
+
+	open my $fic, '<', $sam || die "cannot open $sam $!\n";
+	open my $accepted, '>', $fastq_accepted || die "cannot create $fastq_accepted $! \n";
+	open my $unique, '>', $fastq_accepted_unique || die "cannot create $fastq_accepted_unique $! \n";
+	open my $rejected, '>', $fastq_rejected || die "cannot create $fastq_rejected $! \n";
+	open my $sam_uni, '>', $sam_unique || die "cannot create $sam_unique $! \n";
+	my $sequence = '';
+	while(<$fic>)
+	{
+		chomp $_;
+		if ($_ =~ /^\@[A-Za-z][A-Za-z](\t[A-Za-z][A-Za-z0-9]:[ -~]+)+$/ || $_ =~ /^\@CO\t.*/ )
+		{
+			if ($_ =~ /\@SQ\tSN:(.*)\tLN:(\d*)/)
+			{
+				$size{$1} = $2;
+				$unique_number{$1} = 0;
+				$number{$1} = 0;
+				$numberNM{$1} = 0;
+				$numberM{$1} = 0;
+			}
+			print $sam_uni $_."\n";
+			next;
+		}
+		$reads++;
+		my @line = split (/\t/,$_);
+		$sequence = $line[9];
+		if ($line[1] & 16)
+		{
+			$sequence =reverse($sequence);
+			$sequence =~ tr/atgcuATGCU/tacgaTACGA/;
+		}
+		if ($line[1] == 16 || $line[1] == 0)
+		{
+			my $len = length($sequence);
+			$size_num{$len} ++;
+			$size_num_spe{$line[2]}{$len}++;
+			$mappers ++;
+
+			${$best_hit_number_hashR}{$sequence} = $1  if  ($line[13] =~ /X0:i:(\d*)/ ||  $line[14] =~/X0:i:(\d*)/ );
+			${$duplicate_hashR}{$sequence}++;
+			$number{$line[2]}++;
+			$numberSens{$line[2]}++ if $line[1] == 0 ;
+			$numberReverse{$line[2]}++ if $line[1] == 16 ;
+			print $accepted "\@".$line[0]."\n".$sequence."\n+\n".$line[10]."\n";
+
+			if ($line[11] eq "XT:A:U")
+			{
+				$unique_number{$line[2]}++;
+				$mappersUnique++;
+				print $unique "\@".$line[0]."\n".$sequence."\n+\n".$line[10]."\n";
+				print $sam_uni $_."\n";
+			}
+			if ($_ =~ /.*XM:i:(\d+).*/)
+			{
+				if ($1 == 0){$numberNM{$line[2]}++;}else{$numberM{$line[2]}++;}
+			}
+		}
+		else
+		{
+			${$best_hit_number_hashR}{$sequence} = 0;
+			${$duplicate_hashR}{$sequence}++;
+			print $rejected "\@".$line[0]."\n".$sequence."\n+\n".$line[10]."\n";
+		}
+	}
+	close $fic; close $accepted; close $unique; close $rejected; close $sam_uni;
+
+	print $report "Parsing $sam file\n";
+  print $report "\treads: $reads\n";	
+	print $report "\tmappers: $mappers\n";
+	print $report "\tunique mappers: $mappersUnique\n";
+	print $report "-----------------------------\n";
+	return (\%number, \%unique_number, \%numberSens, \%numberReverse, \%size, $mappers, $mappersUnique, \%size_num, \%size_num_spe, \%numberNM, \%numberM );
+}
+
+sub get_hash_alignment
+{
+  my ($index, $mismatches, $accept, $reject, $outA, $outR, $fastq, $number_of_cpus, $name, $sam, $report, $fai_f) = @_ ;
+  my ($reads, $mappers, $unmapped) = (0,0,0);
+  my $accep_unique;
+  BWA_call ( $index, $fastq, $sam, $mismatches, $number_of_cpus, $report );
+  
+  open my $fic, '<', $sam || die "cannot open $sam $!\n";
+  open my $accepted, '>', $outA || die "cannot open $outA\n"  if $accept == 1;
+  open my $rejected, '>', $outR || die "cannot open $outR\n"  if $reject == 1; 
+  open my $fai, '>', $fai_f || die "cannot open $fai_f\n" if $fai_f;
+  #if ($name eq "snRNAs") {
+  #  open ( $accep_unique, ">".$1."-unique.fastq") if $outR =~ /(.*)\.fastq/;
+  #} 
+  my $sequence = '';
+  while(<$fic>)
+  {
+    chomp $_;
+    if( $_ =~ /^\@[A-Za-z][A-Za-z](\t[A-Za-z][A-Za-z0-9]:[ -~]+)+$/ || $_ =~ /^\@CO\t.*/ )
+    {
+    	if ($fai_f && $_ =~ /\@SQ\tSN:(.*)\tLN:(\d*)/)
+      {
+        print $fai $1."\t".$2."\n";
+      }
+      next;
+    }
+    $reads++;
+    my @line = split (/\t/,$_);
+    $sequence = $line[9];
+    if ($line[1] & 16)
+    {
+      $sequence =reverse($sequence);
+      $sequence =~ tr/atgcuATGCU/tacgaTACGA/;
+    }
+    if ($line[1] & 16 || $line[1] == 0)
+    {
+      $mappers ++;
+      if ($accept == 1 )
+      {
+        print $accepted "\@".$line[0]."\n".$sequence."\n+\n".$line[10]."\n";
+   #     print $accep_unique "\@".$line[0]."\n".$sequence."\n+\n".$line[10]."\n" if ($name eq "snRNAs" && $line[11] eq "XT:A:U"); 
+      }
+    }
+    else
+    {
+      print $rejected "\@".$line[0]."\n".$sequence."\n+\n".$line[10]."\n" if $reject == 1;
+      $unmapped++;
+    }
+  }
+ # close $accep_unique if ($name eq "bonafide_reads");
+  close $fic;
+  close $accepted  if $accept == 1;
+  close $rejected if $reject ==1;
+  close $fai if $fai_f;
+  print $report "\treads: $reads\n";
+  print $report "\tmappers: $mappers\n";
+  print $report "\tunmapped: $unmapped\n";
+  print $report "-----------------------------\n";
+  return ($mappers, $unmapped);
+}
+
+sub sam_count
+{
+  my $sam = shift;
+  my ( %number, %size );
+  
+  open  my $fic, '<', $sam || die "cannot open $sam file $!\n"; 
+  while(<$fic>)
+  {
+    chomp $_;
+    if ($_ =~ /^\@[A-Za-z][A-Za-z](\t[A-Za-z][A-Za-z0-9]:[ -~]+)+$/ || $_ =~ /^\@CO\t.*/ )
+    {
+      if ($_ =~ /\@SQ\tSN:(.*)\tLN:(\d*)/)
+      {
+        $size{$1} = $2;
+        $number{$1} = 0;
+      }      
+    }
+    else
+    {
+  		my @line = split (/\t/,$_);
+ 	  	if ( $line[1]  & 16 || $line[1] == 0 )
+ 	  	{
+ 	  		$number{$line[2]}++;
+ 	  	}
+ 	 	}
+	}
+  close $fic;
+  return ( \%number, \%size );
+}
+
+sub sam_count_mis 
+{
+
+	my $sam = shift;
+	my ( %number, %numberNM, %numberM, %size);
+	
+	open  my $fic, '<', $sam || die "cannot open $sam file $!\n";
+  while(<$fic>)
+  {
+		chomp $_;
+    if ($_ =~ /^\@[A-Za-z][A-Za-z](\t[A-Za-z][A-Za-z0-9]:[ -~]+)+$/ || $_ =~ /^\@CO\t.*/ )
+    {
+      if ($_ =~ /\@SQ\tSN:(.*)\tLN:(\d*)/)
+      {
+				$size{$1} = $2;
+				$number{$1} = 0;
+				$numberNM{$1} = 0;
+				$numberM{$1} = 0;
+			}
+		}
+		else
+		{
+			my @line = split (/\t/,$_);
+			if ( $line[1]  & 16 || $line[1] == 0 )
+			{
+				$number{ $line[2] }++;
+    	 	if ($_ =~ /.*XM:i:(\d+).*/)
+    	 	{
+        	if ( $1 == 0 ){ $numberNM{$line[2]}++; } else { $numberM{$line[2]}++; } 
+      	}
+			}
+		}
+	}
+	return (\%number, \%size, \%numberNM, \%numberM );
+}
+
+sub sam_to_bam_bg
+{
+	my ( $sam, $scale, $number_of_cpus ) = @_;
+	my ( $bam_sorted, $bedgraphM, $bedgraphP, $view_err, $sort_err ) = ( '', '', '', '', '' );
+	if ( $sam =~ /(.*?).sam$/ )
+	{
+		$bam_sorted = $1.'_sorted.bam';
+		$bedgraphP= $1.'_plus.bedgraph';
+		$bedgraphM = $1.'_minus.bedgraph';
+		$view_err = $1.'_view.err';
+		$sort_err = $1.'_sort.err';
+	}	
+	`samtools view -Shb   --threads $number_of_cpus $sam 2> $view_err | samtools sort  -O BAM --threads $number_of_cpus  /dev/stdin 2> $sort_err  > $bam_sorted`;
+	`bedtools genomecov -scale $scale -strand + -bga -ibam $bam_sorted > $bedgraphP`;	
+	`bedtools genomecov -scale $scale -strand - -bga -ibam $bam_sorted > $bedgraphM`;
+}
+
+sub sam_sorted_bam
+{
+	my ( $sam, $number_of_cpus ) = @_;
+	my ( $bam_sorted, $view_err, $sort_err ) = ( '', '', '' );
+	if ( $sam =~ /(.*?).sam$/ )
+	{
+		$bam_sorted = $1.'_sorted.bam';
+		$view_err = $1.'_view.err';
+		$sort_err = $1.'_sort.err';
+
+	}
+	`samtools view -Shb   --threads $number_of_cpus $sam 2> $view_err | samtools sort  -O BAM --threads $number_of_cpus  /dev/stdin  2> $sort_err  > $bam_sorted`;
+}
+
+sub BWA_call
+{
+	my ( $index, $fastq, $sam, $mismatches, $number_of_cpus, $report ) = @_;
+	my ( $aln_err, $samse_err, $seq_num ) = ( $sam.'_aln.err', $sam.'_samse.err', 0 );
+	print $report "-----------------------------\n";
+	print $report "bwa aln -t $number_of_cpus -n $mismatches $index $fastq 2> $aln_err | bwa samse $index /dev/stdin $fastq 2> $samse_err > $sam\n";
+	`bwa aln -t $number_of_cpus -n $mismatches $index $fastq 2> $aln_err | bwa samse $index /dev/stdin $fastq 2> $samse_err > $sam `;
+}
+
+sub rpms_rpkm
+{
+  my ( $counthashR, $sizehashR, $mapped, $out_file, $piRNA_number, $miRNA_number, $bonafide_number ) =@_;
+  open(my $out, ">".$out_file) || die "cannot open normalized file $! \n";
+  print $out "ID\treads counts\tRPKM";
+  print $out "\tper million of piRNAs" if ($piRNA_number != 0);
+  print $out "\tper million of miRNAs" if ($miRNA_number != 0);
+  print $out "\tper million of bonafide reads" if ($bonafide_number != 0);
+  print $out "\n";
+  foreach my $k  ( sort keys %{$counthashR} )
+  {
+    my ($rpkm, $pirna, $mirna, $bonafide) = (0,0,0,0);
+    
+    $rpkm = ( $counthashR->{$k} * 1000000000) / ( $sizehashR->{$k} * $mapped) if ( $sizehashR->{$k} * $mapped) != 0 ;
+    print $out $k."\t".$counthashR->{$k}."\t"; printf $out "%.2f",$rpkm;
+    
+    if ($piRNA_number != 0 )
+    {
+      $pirna = ( $counthashR->{$k}  * 1000000) / $piRNA_number;
+      printf $out "\t%.2f",$pirna;
+    }
+    if ($miRNA_number != 0 )
+    {
+      $mirna = ( $counthashR->{$k}  * 1000000) / $miRNA_number;
+      printf $out "\t%.2f",$mirna;
+    }
+    if ($bonafide_number != 0 )
+    {
+      $bonafide = ( $counthashR->{$k}  * 1000000) / $bonafide_number;
+      printf $out "\t%.2f",$bonafide;
+    }
+    print $out "\n";
+ 	}
+  close $out;
+}
+
+sub extract_sam
+{
+  my ( $hashRef, $sam_in, $sam_out, $sam_uni_out, $fastq_out, $fastq_uni_out ) = @_;
+  
+	open my $s_in, '<', $sam_in || die "cannot open $sam_in file $!\n";
+
+  open my $f_out, '>', $fastq_out || die "cannot create $fastq_out $!\n"; 
+  open my $f_uni_out, '>', $fastq_uni_out || die "cannot create $fastq_uni_out $!\n"; 
+  
+  open my $s_out, '>', $sam_out || die "cannot create $sam_out file $!\n" if defined ($hashRef);
+  open my $s_uni_out, '>', $sam_uni_out || die "cannot create $sam_uni_out file $!\n";
+
+  my $sequence = '';
+  while(<$s_in>)
+  {
+    if ($_ =~ /^\@[A-Za-z][A-Za-z](\t[A-Za-z][A-Za-z0-9]:[ -~]+)+$/ || $_ =~ /^\@CO\t.*/ )
+    {
+      print $s_out $_ if defined ($hashRef);
+      print $s_uni_out $_;
+      next;
+    }
+    my @line = split (/\t/,$_);
+    $sequence = $line[0];
+    if ( (! defined ($hashRef) )|| (  exists $hashRef->{$sequence}  &&  $hashRef->{$sequence} == 1 ) )
+    {
+      my $arn  =  $line[9];
+      if ($line[1] & 16)
+      {
+        $arn =reverse($arn);
+        $arn =~ tr/atgcuATGCU/tacgaTACGA/;
+      }
+
+      if  ( ( $line[1] == 16 || $line[1] == 0 ) )
+			{
+      	print $f_out "\@".$line[0]."\n".$arn."\n+\n".$line[10]."\n" ;
+      	print $s_out $_ if defined ($hashRef);
+      	if ( $line[11] eq "XT:A:U" )
+      	{
+      		print $f_uni_out "\@".$line[0]."\n".$arn."\n+\n".$line[10]."\n" ;
+      		print $s_uni_out $_ ;
+      	}
+      }
+    } 
+  }
+  close $s_in; close $s_out if defined ($hashRef); 
+  close $s_uni_out; close $f_out; close $f_uni_out;
+}
+
+sub get_fastq_seq
+{
+  my $fastq = shift;
+  my %hash; my $cmp = 0; 
+
+  open my $fic, '<', $fastq || die "cannot open input file $! \n";
+  while(<$fic>)
+  {
+    chomp $_;
+    $cmp++;
+    if ($cmp % 4 == 1)
+    {
+      die "file do not contain a @ at line $cmp\n" unless ($_ =~ /^\@/ );
+      if ($_ =~ /^\@(.*)\s.*/) { $hash{$1} = 1;}
+      elsif ($_ =~ /^\@(.*)/) { $hash{$1} = 1;}
+    }
+    elsif ($cmp % 4 == 3 )
+    {
+      die "file do not contain a + at line $cmp\n" unless $_ =~ /^\+/;
+    }
+  }
+  close $fic;
+  return \%hash;
+}
+
+1;