Mercurial > repos > fcaramia > contra

annotate contra_wrapper.pl @ 23:2770f49cb0dc

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re-uploading contra
author Franco Caramia <franco.caramia@petermac.org>
date Tue, 20 May 2014 09:59:00 +1000
parents
children c361b3fb806e
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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23
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
1 use strict;
2770f49cb0dc re-uploading contra
Franco Caramia <franco.caramia@petermac.org>
parents:
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2 use warnings;
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Franco Caramia <franco.caramia@petermac.org>
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3
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Franco Caramia <franco.caramia@petermac.org>
parents:
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4 use FindBin;
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Franco Caramia <franco.caramia@petermac.org>
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5 use File::Path qw(make_path);
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Franco Caramia <franco.caramia@petermac.org>
parents:
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6 use File::Spec;
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Franco Caramia <franco.caramia@petermac.org>
parents:
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7
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Franco Caramia <franco.caramia@petermac.org>
parents:
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8
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Franco Caramia <franco.caramia@petermac.org>
parents:
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9 die "Bad number of inputs" if(!@ARGV);
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Franco Caramia <franco.caramia@petermac.org>
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10
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Franco Caramia <franco.caramia@petermac.org>
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11 my $player_options = "";
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Franco Caramia <franco.caramia@petermac.org>
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12 my $contra_output;
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Franco Caramia <franco.caramia@petermac.org>
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13 my $contra_dir;
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Franco Caramia <franco.caramia@petermac.org>
parents:
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14
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Franco Caramia <franco.caramia@petermac.org>
parents:
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15
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Franco Caramia <franco.caramia@petermac.org>
parents:
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16
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Franco Caramia <franco.caramia@petermac.org>
parents:
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17 foreach my $input (@ARGV)
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Franco Caramia <franco.caramia@petermac.org>
parents:
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18 {
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Franco Caramia <franco.caramia@petermac.org>
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19 my @tmp = split "::", $input;
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Franco Caramia <franco.caramia@petermac.org>
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20
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Franco Caramia <franco.caramia@petermac.org>
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21 if($tmp[0] eq "PLAYEROPTION")
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Franco Caramia <franco.caramia@petermac.org>
parents:
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22 {
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Franco Caramia <franco.caramia@petermac.org>
parents:
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23 my $variable = $tmp[1];
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Franco Caramia <franco.caramia@petermac.org>
parents:
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24 $variable =~ s/=/ /g;
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Franco Caramia <franco.caramia@petermac.org>
parents:
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25 print "$variable\n";
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Franco Caramia <franco.caramia@petermac.org>
parents:
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26 $player_options = "$player_options $variable";
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Franco Caramia <franco.caramia@petermac.org>
parents:
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27 }
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Franco Caramia <franco.caramia@petermac.org>
parents:
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28 elsif($tmp[0] eq "CONTRAOUTPUT")
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Franco Caramia <franco.caramia@petermac.org>
parents:
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29 {
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Franco Caramia <franco.caramia@petermac.org>
parents:
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30 $contra_output = $tmp[1];
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Franco Caramia <franco.caramia@petermac.org>
parents:
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31 }
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Franco Caramia <franco.caramia@petermac.org>
parents:
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32 elsif($tmp[0] eq "CONTRADIR")
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Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
33 {
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Franco Caramia <franco.caramia@petermac.org>
parents:
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34 $contra_dir = $tmp[1];
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Franco Caramia <franco.caramia@petermac.org>
parents:
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35 }
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Franco Caramia <franco.caramia@petermac.org>
parents:
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36 else
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Franco Caramia <franco.caramia@petermac.org>
parents:
diff changeset
37 {
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Franco Caramia <franco.caramia@petermac.org>
parents:
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38 die("Unknown input: $input\n");
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Franco Caramia <franco.caramia@petermac.org>
parents:
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39 }
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Franco Caramia <franco.caramia@petermac.org>
parents:
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40 }
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Franco Caramia <franco.caramia@petermac.org>
parents:
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41
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Franco Caramia <franco.caramia@petermac.org>
parents:
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42
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Franco Caramia <franco.caramia@petermac.org>
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43 my $working_dir = "CONTRA_OUTPUT";
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Franco Caramia <franco.caramia@petermac.org>
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44 make_path($contra_dir);
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Franco Caramia <franco.caramia@petermac.org>
parents:
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45 #remove extension
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Franco Caramia <franco.caramia@petermac.org>
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46
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Franco Caramia <franco.caramia@petermac.org>
parents:
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47 #run contra
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Franco Caramia <franco.caramia@petermac.org>
parents:
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48 system(File::Spec->catfile($FindBin::Bin, 'contra.py') . " -o $working_dir $player_options > /dev/null 2>&1");
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Franco Caramia <franco.caramia@petermac.org>
parents:
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49
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Franco Caramia <franco.caramia@petermac.org>
parents:
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50 #set html
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Franco Caramia <franco.caramia@petermac.org>
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51 #print "$contra_output - $working_dir\n";
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Franco Caramia <franco.caramia@petermac.org>
parents:
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52 open(HTML, ">$contra_output");
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Franco Caramia <franco.caramia@petermac.org>
parents:
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53 print HTML "<html><head><title>Contra: Copy Number Analysis for Targeted Resequencing</title></head><body><h3>Contra Output Files:</h3><p><ul>\n";
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Franco Caramia <franco.caramia@petermac.org>
parents:
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54 move_files($working_dir);
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Franco Caramia <franco.caramia@petermac.org>
parents:
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55 print HTML "</ul></p>\n";
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Franco Caramia <franco.caramia@petermac.org>
parents:
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56 close(HTML);
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Franco Caramia <franco.caramia@petermac.org>
parents:
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57
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Franco Caramia <franco.caramia@petermac.org>
parents:
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58 sub move_files
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Franco Caramia <franco.caramia@petermac.org>
parents:
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59 {
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Franco Caramia <franco.caramia@petermac.org>
parents:
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60 my $local_dir = $_[0];
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Franco Caramia <franco.caramia@petermac.org>
parents:
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61 opendir(DIR, $local_dir);
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Franco Caramia <franco.caramia@petermac.org>
parents:
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62 #print ("Openning: $local_dir\n");
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Franco Caramia <franco.caramia@petermac.org>
parents:
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63 my @FILES= readdir(DIR);
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Franco Caramia <franco.caramia@petermac.org>
parents:
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64 closedir(DIR);
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Franco Caramia <franco.caramia@petermac.org>
parents:
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65 foreach my $file (@FILES)
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Franco Caramia <franco.caramia@petermac.org>
parents:
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66 {
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Franco Caramia <franco.caramia@petermac.org>
parents:
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67 if ($file eq "." || $file eq "..")
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Franco Caramia <franco.caramia@petermac.org>
parents:
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68 {
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Franco Caramia <franco.caramia@petermac.org>
parents:
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69 #print ("./ or ../ skipped\n");
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Franco Caramia <franco.caramia@petermac.org>
parents:
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70 }
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Franco Caramia <franco.caramia@petermac.org>
parents:
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71 elsif (-d "$local_dir/$file")
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Franco Caramia <franco.caramia@petermac.org>
parents:
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72 {
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Franco Caramia <franco.caramia@petermac.org>
parents:
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73 #print ("moving to: $local_dir/$file\n");
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Franco Caramia <franco.caramia@petermac.org>
parents:
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74 move_files("$local_dir/$file");
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Franco Caramia <franco.caramia@petermac.org>
parents:
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75 }
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Franco Caramia <franco.caramia@petermac.org>
parents:
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76 elsif (-f "$local_dir/$file")
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Franco Caramia <franco.caramia@petermac.org>
parents:
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77 {
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Franco Caramia <franco.caramia@petermac.org>
parents:
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78 #print ("mv $local_dir/$file $contra_dir\n");
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Franco Caramia <franco.caramia@petermac.org>
parents:
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79 print HTML "<li><a href=$file>$file</a></li>\n";
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Franco Caramia <franco.caramia@petermac.org>
parents:
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80 system ("mv $local_dir/$file $contra_dir");
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Franco Caramia <franco.caramia@petermac.org>
parents:
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81 }
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Franco Caramia <franco.caramia@petermac.org>
parents:
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82 else
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Franco Caramia <franco.caramia@petermac.org>
parents:
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83 {
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Franco Caramia <franco.caramia@petermac.org>
parents:
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84 die("Unrecognized file generated: $file\n");
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Franco Caramia <franco.caramia@petermac.org>
parents:
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85 }
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Franco Caramia <franco.caramia@petermac.org>
parents:
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86
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Franco Caramia <franco.caramia@petermac.org>
parents:
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87
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Franco Caramia <franco.caramia@petermac.org>
parents:
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88 }
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Franco Caramia <franco.caramia@petermac.org>
parents:
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89
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Franco Caramia <franco.caramia@petermac.org>
parents:
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90 }
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Franco Caramia <franco.caramia@petermac.org>
parents:
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91