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1 #!/usr/bin/env perl
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2
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3 # Author: Johannes T. Roehr
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4
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5 use warnings;
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6 use strict;
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7
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8 my $flexbarDir = "";
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9
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10 my $pwd = $ENV{PWD};
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11
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12 my $lastIdx = $#ARGV;
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13 my $format = $ARGV[$lastIdx];
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14 my $folder = $ARGV[$lastIdx - 1];
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15 my $id = $ARGV[$lastIdx - 2];
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16 my $outFile = $ARGV[$lastIdx - 3];
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17
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18 my $call = join " ", @ARGV[0..($lastIdx - 4)];
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19
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20 system $flexbarDir . $call .' --target reads > '. $outFile;
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21
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22 foreach(<$pwd ."/reads"*>){
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23
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24 if(/^\.\//){
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25 my $file = $pwd ."/". $_;
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26
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27 s/^\.\///;
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28 my $fileType;
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29
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30 $fileType = $1 if /\.(\w+)$/;
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31 $fileType = $format if /\.\w+fast\w$/;
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32 $fileType = 'tabular' if $fileType eq 'lengthdist';
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33
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34 s/_//g;
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35
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36 my $name = "primary_". $id ."_". $_ ."_visible_". $fileType;
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37
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38 rename $file, $name;
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39 rename $name, $folder;
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40 }
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41 }
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42
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