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1 use strict;
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2 use warnings;
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3 use File::Basename;
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4 use Cwd;
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5 use File::Path qw(make_path remove_tree);
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6 die qq(
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7 Bad numbr of inputs
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8
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9 ) if(!@ARGV);
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10
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11
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12 my $player_options = "";
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13 my $contra_output;
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14 my $contra_dir;
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15
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16 my $dir = getcwd;
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17 my $variable;
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18
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19 foreach my $input (@ARGV)
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20 {
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21 my @tmp = split "::", $input;
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22
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23 if($tmp[0] eq "PLAYEROPTION")
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24 {
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25 $variable = $tmp[1];
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26 $variable =~ s/=/ /g;
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27 print "$variable\n";
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28 $player_options = "$player_options $variable";
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29 }
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30 elsif($tmp[0] eq "CONTRAOUTPUT")
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31 {
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32 $contra_output = $tmp[1];
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33 }
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34 elsif($tmp[0] eq "CONTRADIR")
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35 {
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36 $contra_dir = $tmp[1];
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37 }
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38 else
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39 {
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40 die("Unknown Input: $input\n");
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41 }
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42 }
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43
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44
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45 my $working_dir = "CONTRA_OUTPUT";
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46 make_path($contra_dir);
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47 #remove extension
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48
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49 #run contra
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50 system ("contra.py -o $working_dir $player_options > /dev/null 2>&1");
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51
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52
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53 #set html
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54 #print "$contra_output - $working_dir\n";
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55 open(HTML, ">$contra_output");
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56 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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57 move_files($working_dir);
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58 print HTML "</ul></p>\n";
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59 close(HTML);
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60
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61 sub move_files
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62 {
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63 my $local_dir = $_[0];
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64 opendir(DIR, $local_dir);
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65 #print ("Openning: $local_dir\n");
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66 my @FILES= readdir(DIR);
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67 closedir(DIR);
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68 foreach my $file (@FILES)
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69 {
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70 if ($file eq "." || $file eq "..")
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71 {
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72 #print ("./ or ../ skipped\n");
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73 }
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74 elsif (-d "$local_dir/$file")
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75 {
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76 #print ("moving to: $local_dir/$file\n");
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77 move_files("$local_dir/$file");
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78 }
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79 elsif (-f "$local_dir/$file")
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80 {
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81 #print ("mv $local_dir/$file $contra_dir\n");
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82 print HTML "<li><a href=$file>$file</a></li>\n";
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83 system ("mv $local_dir/$file $contra_dir");
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84 }
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85 else
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86 {
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87 die("Unrecognized file generated: $file\n");
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88 }
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89
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90
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91 }
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92
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93 }
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94
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