annotate bin/resize.pm @ 15:16c3c1b0362a draft

Uploaded

package resize;

use strict;
use warnings;

use FindBin;
use lib $FindBin::Bin;
use Rcall qw ( histogram );

use Exporter;
our @ISA = qw( Exporter );
our @EXPORT_OK = qw( &size_distribution );

sub size_distribution
{
  my ( $fastq, $fastq_out, $dir, $min, $max ) = @_;

  my ( %fragments_size, %duplicates ) ;
  my $num = size($min, $max, $fastq, $fastq_out, \%fragments_size, \%duplicates);

  my $png = $dir.'histogram.png';
   histogram(\%fragments_size, $png, $num);
  
  my $size = $dir.'reads_size.txt';
  

  my $pourcentage;
  open  my $o, '>', $size || die "cannot open $size $!\n";
  print $o "size\tnumber\tpercentage\n";
  foreach my  $k (sort { $a <=> $b } keys %fragments_size )
  {
    $pourcentage = $fragments_size{$k} / $num * 100;
    
    print $o "$k\t$fragments_size{$k}\t";
    printf $o "%.2f\n",$pourcentage;
  }
  close $o;
  
  my $dup = $dir.'duplicates.txt' ;  
  open $o, '>', $dup || die "cannot open $size $!\n";
  print $o "size\tnumber\n";
  foreach my  $k (sort { $duplicates{$b} <=> $duplicates{$a} } keys %duplicates )
  {
    print $o "$k\t$duplicates{$k}\n";
  }
  close $o;
}

sub size
{
  my ($min, $max, $in_file, $out_file, $sizeHashR, $duplicateHashR) = @_;
  my ($numreads, $size, $cmp, $ok, $line) = (0, 0, 0, 0);
  my @fastq;
  open (my $in, $in_file) || die "cannot open $in_file $!\n";
  open (my $out, ">".$out_file)  || die "cannot create $out_file $!\n";
  while(<$in>)
  {
    chomp $_;
    $cmp++; $line++;
    if ($cmp == 1)
    {
      die "file do not contain a @ at line $line\n" unless ($_ =~ /^\@/ );
      $ok = 0; @fastq = ();
      push(@fastq,$_);
    }
    elsif ($cmp == 2)
    {
      #die "unrecognized symbol at line $line\n" unless ($_ =~ /[atcgATCGnN]+/ || $_ =~ /^$/ );
      push(@fastq,$_);
      $size = length($_);
      if ($size >= $min && $size <= $max)
      {
        $numreads++;
        ${$sizeHashR}{$size}+=1;
        ${$duplicateHashR}{$_}+=1 if (defined($duplicateHashR));
        $ok = 1;
      }
    }
    elsif ($cmp == 3 )
    {
      die "file do not contain a + at line $line\n" unless $_ =~ /^\+/;
      push(@fastq,$_);
    }
    elsif ($cmp == 4 )
    {
      push(@fastq,$_);
      $cmp = 0;
      if ($ok == 1)
      {
        foreach my $t (@fastq)
        {
          print $out $t."\n";
        }
      }
    }
  }
  close $in; close $out;
  return $numreads;
}

1;