Mercurial > repos > brasset_jensen > srnapipe

annotate lib/sRNAPipe/resize.pm @ 65:0e9adbd82bb4 draft

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planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit a623ac00600191204ede63c45862a7fbb561afd2
author brasset_jensen
date Wed, 30 Jan 2019 02:41:24 -0500
parents 967512924317
children
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64
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
parents:
diff changeset
1 package sRNAPipe::resize;
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
parents:
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2
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
parents:
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3 use strict;
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
parents:
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4 use warnings;
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
parents:
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967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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6 use FindBin;
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
parents:
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7 use lib "$FindBin::Bin/../lib";
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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8 use sRNAPipe::Rcall qw ( histogram );
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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10 use Exporter;
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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11 our @ISA = qw( Exporter );
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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12 our @EXPORT_OK = qw( &size_distribution );
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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14 sub size_distribution
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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15 {
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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16 my ( $fastq, $fastq_out, $dir, $min, $max ) = @_;
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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18 my ( %fragments_size, %duplicates ) ;
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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19 my $num = size($min, $max, $fastq, $fastq_out, \%fragments_size, \%duplicates);
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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21 my $png = $dir.'histogram.png';
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
parents:
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22 histogram(\%fragments_size, $png, $num);
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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24 my $size = $dir.'reads_size.txt';
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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27 my $pourcentage;
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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28 open my $o, '>', $size || die "cannot open $size $!\n";
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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29 print $o "size\tnumber\tpercentage\n";
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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30 foreach my $k (sort { $a <=> $b } keys %fragments_size )
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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31 {
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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32 $pourcentage = $fragments_size{$k} / $num * 100;
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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34 print $o "$k\t$fragments_size{$k}\t";
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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35 printf $o "%.2f\n",$pourcentage;
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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36 }
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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37 close $o;
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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39 my $dup = $dir.'duplicates.txt' ;
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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40 open $o, '>', $dup || die "cannot open $size $!\n";
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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41 print $o "size\tnumber\n";
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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42 foreach my $k (sort { $duplicates{$b} <=> $duplicates{$a} } keys %duplicates )
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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43 {
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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44 print $o "$k\t$duplicates{$k}\n";
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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45 }
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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46 close $o;
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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47 }
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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49 sub size
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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50 {
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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51 my ($min, $max, $in_file, $out_file, $sizeHashR, $duplicateHashR) = @_;
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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52 my ($numreads, $size, $cmp, $ok, $line) = (0, 0, 0, 0);
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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53 my @fastq;
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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54 open (my $in, $in_file) || die "cannot open $in_file $!\n";
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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55 open (my $out, ">".$out_file) || die "cannot create $out_file $!\n";
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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56 while(<$in>)
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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57 {
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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58 chomp $_;
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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59 $cmp++; $line++;
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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60 if ($cmp == 1)
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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61 {
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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62 die "file do not contain a @ at line $line\n" unless ($_ =~ /^\@/ );
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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63 $ok = 0; @fastq = ();
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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64 push(@fastq,$_);
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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65 }
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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66 elsif ($cmp == 2)
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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67 {
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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68 #die "unrecognized symbol at line $line\n" unless ($_ =~ /[atcgATCGnN]+/ || $_ =~ /^$/ );
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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69 push(@fastq,$_);
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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70 $size = length($_);
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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71 if ($size >= $min && $size <= $max)
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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72 {
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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73 $numreads++;
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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74 ${$sizeHashR}{$size}+=1;
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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75 ${$duplicateHashR}{$_}+=1 if (defined($duplicateHashR));
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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76 $ok = 1;
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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77 }
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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78 }
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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79 elsif ($cmp == 3 )
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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80 {
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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81 die "file do not contain a + at line $line\n" unless $_ =~ /^\+/;
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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82 push(@fastq,$_);
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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83 }
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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84 elsif ($cmp == 4 )
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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85 {
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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86 push(@fastq,$_);
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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87 $cmp = 0;
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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88 if ($ok == 1)
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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89 {
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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90 foreach my $t (@fastq)
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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91 {
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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92 print $out $t."\n";
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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93 }
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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94 }
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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95 }
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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96 }
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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97 close $in; close $out;
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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98 return $numreads;
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
parents:
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99 }
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
parents:
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100
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
parents:
diff changeset
101 1;