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1 #!/usr/bin/perl
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2 use strict;
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3 use Getopt::Long;
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4 use vars qw($opt_reference $opt_input $opt_output @opt_zygosity @opt_vartype @opt_varscorevaf @opt_varscoreeaf @opt_varquality);
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5 $| = 1; # set autoflush to screen
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6
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7 # This is a wrapper for the cgatools varfilter function to run cgatools varfilter in Galaxy.
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8 # The wrapper generates the filter(s) in the correct format to be used with the input file.
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9 # written 6-1-2012 by bcrain@completegenomics.com
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10
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11
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12 #print join("\n", @ARGV), "\n";
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13 &GetOptions("reference=s", "input=s", "output=s", "zygosity=s@", "vartype=s@", "varscorevaf=s@", "varscoreeaf=s@", "varquality=s@");
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14
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15 my $append = '';
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16
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17 for (my $i = 0; $i <= $#opt_zygosity; $i ++)
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18 {
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19 my $filter = '';
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20 unless ($opt_zygosity[$i] eq 'NA') {$filter = $opt_zygosity[$i];}
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21 unless ($opt_vartype[$i] eq 'NA')
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22 {
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23 $filter ne '' and $filter .= ':';
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24 $filter .= 'varType=' . $opt_vartype[$i];
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25 }
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26 unless ($opt_varscorevaf[$i] eq 'x')
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27 {
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28 $filter ne '' and $filter .= ':';
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29 $opt_varscorevaf[$i] =~ s/^x//;
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30 $filter .= 'varScoreVAF<' . $opt_varscorevaf[$i];
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31 }
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32 unless ($opt_varscoreeaf[$i] eq 'x')
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33 {
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34 $filter ne '' and $filter .= ':';
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35 $opt_varscoreeaf[$i] =~ s/^x//;
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36 $filter .= 'varScoreEAF<' . $opt_varscoreeaf[$i];
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37 }
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38 unless ($opt_varquality[$i] eq 'NA')
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39 {
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40 $filter ne '' and $filter .= ':';
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41 $filter .= 'varQuality!=' . $opt_varquality[$i];
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42 }
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43
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44 if ($filter ne '')
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45 {
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46 if ($append eq '') {$append = '#' . $filter;}
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47 else {$append .= ',' . $filter;}
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48 }
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49 }
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50 print "cgatools varfilter
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51 --beta
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52 --reference $opt_reference
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53 --output $opt_output
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54 --input '${opt_input}${append}'\n";
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55
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56 `cgatools varfilter --beta --reference $opt_reference --output $opt_output --input '${opt_input}${append}'`; |
