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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", "b=s", "out=s", "output_path=s","id=s","m=i", "file_type=s", "both", "r=s", "version", "i");
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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/pyBarcodeFilter.py --version";
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14 }
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15 else{
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16 $cmnd = "python /usr/local/bin/pyBarcodeFilter.py -f $opt{f} -b $opt{b} -m $opt{m} --file_type $opt{file_type}";
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17
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18 if(defined $opt{r}){
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19
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20 $cmnd.= " -r $opt{r}";
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21
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22 if(exists $opt{both}){
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23 $cmnd .= " --both";
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24 }
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25 }
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26
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27 if(exists $opt{i}){
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28 $cmnd .= " -i";
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29 }
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30 }
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31
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32 # Create the output directory (for the multiple output files)
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33 my $output_path = $opt{output_path};
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34
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35 system $cmnd;
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36
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37 open(BC,$opt{b}) || die "Cannot open barcode file";
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38 my %bc;
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39 while(my $line = <BC>){
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40 chomp($line);
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41 my ($barcode,$sample) = (split(/\t/,$line))[0,1];
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42 $bc{$barcode}=$sample;
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43 }
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44
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45 system "mv barcode_statistics.txt $opt{out}";
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46
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47 my $ft = lc($opt{file_type});
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48
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49 foreach my $key(keys %bc){
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50 my @split = (split(/\//,$opt{f}));
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51 my $l = @split;
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52 my $output = $split[$l-1];
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53 $output = (split(/\./,$output))[0];
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54 $output = "$output"."_"."$key"."_"."$bc{$key}"."."."$ft";
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55 my $rename = "$output_path/primary_$opt{id}_$bc{$key}-1"."_visible_"."$ft";
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56 system "mv $output $rename";
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57
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58 if(defined $opt{r}){
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59 my @split2 = (split(/\//,$opt{r}));
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60 $l = @split2;
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61 $output = $split2[$l-1];
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62 $output = (split(/\./,$output))[0];
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63 $output = "$output"."_"."$key"."_"."$bc{$key}"."."."$ft";
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64 $rename = "$output_path/primary_$opt{id}_$bc{$key}-2"."_visible_"."$ft";
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65 system "mv $output $rename";
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66 }
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67 }
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68
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69
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70 close BC;
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71
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