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1 #!/usr/bin/perl -w
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2 use strict;
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3 use Getopt::Long;
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4
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5 my %opt;
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6
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7
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8 GetOptions(\%opt, "f=s", "r=s", "o=s", "out2=s", "version","id=s");
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9
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10 my $cmnd;
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11
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12 if (exists $opt{version}){
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13 $cmnd = "python /usr/local/bin/pyFastqDuplicateRemover.py --version";
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14 }
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15 else{
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16 $cmnd = "python /usr/local/bin/pyFastqDuplicateRemover.py -f $opt{f} -o $opt{id}";
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17
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18 if(defined $opt{r}){
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19 $cmnd.= " -r $opt{r}";
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20 }
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21 }
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22
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23 system $cmnd;
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24
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25
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26
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27 if(defined $opt{r}){
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28 system "mv $opt{id}"."_1.fasta $opt{o}";
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29 system "mv $opt{id}"."_2.fasta $opt{out2}";
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30 }
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31 else{
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32 system "mv $opt{id} $opt{o}";
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33 }
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34
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