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1 #!/usr/bin/perl
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2
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3 # trimmomatic_wrapper.pl
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4 #
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5 # Copyright 2012 Simon Gladman<simon.gladman@monash.edu>
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6 #
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7 # This program is free software; you can redistribute it and/or modify
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8 # it under the terms of the GNU General Public License as published by
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9 # the Free Software Foundation; either version 2 of the License, or
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10 # (at your option) any later version.
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11 #
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12 # This program is distributed in the hope that it will be useful,
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13 # but WITHOUT ANY WARRANTY; without even the implied warranty of
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14 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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15 # GNU General Public License for more details.
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16 #
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17 # You should have received a copy of the GNU General Public License
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18 # along with this program; if not, write to the Free Software
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19 # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
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20 # MA 02110-1301, USA.
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21 #
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22 #
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23
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24 use strict;
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25 use warnings;
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26 use File::Temp qw( tempdir tempfile);
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27
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28 my %stuff = @ARGV;
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29
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30 my $dir = tempdir(CLEANUP => 1);
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31 my ($fwdtempfh, $fwdtemp) = tempfile( DIR => $dir );
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32 my ($revtempfh, $revtemp) = tempfile( DIR => $dir );
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33
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34 foreach my $x (keys %stuff){
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35 print "$x\t" . $stuff{$x} . "\n";
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36 }
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37
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38 my $tooldir = $stuff{"tool-dir"};
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39 my $jar = "$tooldir/shared/jars/trimmomatic-0.22.jar";
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40
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41 my $numthreads = 4;
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42
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43
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44 my $cmd = "java -cp $jar org.usadellab.trimmomatic.Trimmomatic";
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45
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46 if($stuff{"paired"} eq "True"){
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47 $cmd .= "PE";
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48 }
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49 else {
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50 $cmd .= "SE";
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51 }
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52
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53 $cmd .= " -threads $numthreads";
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54
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55 $cmd .= " -phred33" if($stuff{"phred"} eq "phred33");
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56
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57 if($stuff{"log"} eq "True"){
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58 $cmd .= " -trimlog " . $stuff{"logfile"};
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59 }
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60
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61 if($stuff{"paired"} eq "True"){
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62 $cmd .= " " . join(" ",($stuff{"fwdfile"},$stuff{"revfile"},$stuff{"fwdpairs"},$fwdtemp,$stuff{"revpairs"},$revtemp));
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63 }
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64 else {
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65 $cmd .= " " . join(" ",($stuff{"fwdfile"},$stuff{"singles"}));
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66 }
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67
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68 $cmd .= " " . join(":",("ILLUMINACLIP",$stuff{"adaptfile"},$stuff{"adaptseed"},$stuff{"adaptpalindrome"},$stuff{"adaptsimple"})) if $stuff{"cutadapt"} eq "True";
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69
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70 $cmd .= " " . join(":",("SLIDINGWINDOW",$stuff{"slidingsize"},$stuff{"slidingqual"})) if $stuff{"slidingwindow"} eq "True";
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71
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72 $cmd .= " " .join(":",("LEADING",$stuff{"leadingqual"})) if $stuff{"trimleading"} eq "True";
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73
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74 $cmd .= " " .join(":",("TRAILING",$stuff{"trailingqual"})) if $stuff{"trimtrailing"} eq "True";
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75
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76 $cmd .= " " .join(":",("CROP",$stuff{"croplen"})) if $stuff{"crop"} eq "True";
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77
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78 $cmd .= " " .join(":",("HEADCROP",$stuff{"headcroplen"})) if $stuff{"headcrop"} eq "True";
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79
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80 $cmd .= " " .join(":",("MINLEN",$stuff{"minlen"}));
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81
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82 print "Command:\t$cmd\n";
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83
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84 if(system($cmd) == 0){
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85 if ($stuff{"paired"} eq "True"){
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86 my $catcmd = "cat $fwdtemp $revtemp > " . $stuff{"singles"};
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87 system($catcmd) == 0 or die "Something went wrong with the cat command $!";
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88 }
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89 }
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90 else{
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91 print "There was an error with trimmomatic! $!";
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92 exit(1);
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93 }
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94
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95 exit(0);
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