Mercurial > repos > brasset_jensen > srnapipe

annotate bin/resize.pm @ 61:9185ca0a7b43 draft

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Updated package according to recommendations.
author pierre.pouchin
date Wed, 16 Jan 2019 08:18:13 -0500
parents 4bc00caa60b4
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
61
9185ca0a7b43 Updated package according to recommendations.
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1 package resize;
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2
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3 use strict;
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4 use warnings;
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5
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6 use FindBin;
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7 use lib $FindBin::Bin;
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8 use Rcall qw ( histogram );
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9
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10 use Exporter;
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11 our @ISA = qw( Exporter );
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12 our @EXPORT_OK = qw( &size_distribution );
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13
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14 sub size_distribution
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15 {
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16 my ( $fastq, $fastq_out, $dir, $min, $max ) = @_;
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17
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18 my ( %fragments_size, %duplicates ) ;
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19 my $num = size($min, $max, $fastq, $fastq_out, \%fragments_size, \%duplicates);
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20
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21 my $png = $dir.'histogram.png';
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22 histogram(\%fragments_size, $png, $num);
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23
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24 my $size = $dir.'reads_size.txt';
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25
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26
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27 my $pourcentage;
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28 open my $o, '>', $size || die "cannot open $size $!\n";
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29 print $o "size\tnumber\tpercentage\n";
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30 foreach my $k (sort { $a <=> $b } keys %fragments_size )
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31 {
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32 $pourcentage = $fragments_size{$k} / $num * 100;
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33
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34 print $o "$k\t$fragments_size{$k}\t";
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35 printf $o "%.2f\n",$pourcentage;
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36 }
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37 close $o;
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38
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39 my $dup = $dir.'duplicates.txt' ;
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40 open $o, '>', $dup || die "cannot open $size $!\n";
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41 print $o "size\tnumber\n";
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42 foreach my $k (sort { $duplicates{$b} <=> $duplicates{$a} } keys %duplicates )
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43 {
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44 print $o "$k\t$duplicates{$k}\n";
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45 }
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46 close $o;
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47 }
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48
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49 sub size
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50 {
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51 my ($min, $max, $in_file, $out_file, $sizeHashR, $duplicateHashR) = @_;
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52 my ($numreads, $size, $cmp, $ok, $line) = (0, 0, 0, 0);
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53 my @fastq;
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54 open (my $in, $in_file) || die "cannot open $in_file $!\n";
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55 open (my $out, ">".$out_file) || die "cannot create $out_file $!\n";
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56 while(<$in>)
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57 {
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58 chomp $_;
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59 $cmp++; $line++;
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60 if ($cmp == 1)
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61 {
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62 die "file do not contain a @ at line $line\n" unless ($_ =~ /^\@/ );
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63 $ok = 0; @fastq = ();
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64 push(@fastq,$_);
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65 }
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66 elsif ($cmp == 2)
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67 {
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68 #die "unrecognized symbol at line $line\n" unless ($_ =~ /[atcgATCGnN]+/ || $_ =~ /^$/ );
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69 push(@fastq,$_);
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70 $size = length($_);
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71 if ($size >= $min && $size <= $max)
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72 {
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73 $numreads++;
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74 ${$sizeHashR}{$size}+=1;
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75 ${$duplicateHashR}{$_}+=1 if (defined($duplicateHashR));
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76 $ok = 1;
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77 }
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78 }
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79 elsif ($cmp == 3 )
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80 {
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81 die "file do not contain a + at line $line\n" unless $_ =~ /^\+/;
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82 push(@fastq,$_);
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83 }
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84 elsif ($cmp == 4 )
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85 {
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86 push(@fastq,$_);
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87 $cmp = 0;
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88 if ($ok == 1)
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89 {
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90 foreach my $t (@fastq)
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91 {
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92 print $out $t."\n";
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93 }
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94 }
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95 }
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96 }
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97 close $in; close $out;
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98 return $numreads;
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99 }
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100
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101 1;