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1 #!/usr/bin/perl
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2
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3 # load modules
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4 use Getopt::Std;
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5
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6 ##########################
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7 # COMMAND LINE ARGUMENTS #
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8 ##########################
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9 # v = (v)cf file to load
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10 # V = (V)CF file encoded id
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11 # u = (u)ser email from galaxy
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12 # n = sample (n)ame
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13 # a = sample (a)nnotation
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14 # g = sample (g)ender
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15 # o = (o)utput file (simple text file)
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16 # b = (b)am file (optional)
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17 # B = (B)am index , needed if b is specified
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18 # c = encoded id of bam file (optional)
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19 # C = encoded id of Bam index , needed if b is specified => NOT POSSIBLE YET, NEEDS INDEXING ON VARIANTDB SERVER !
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20 # S = (S)erver addrress to send data to.
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21 # R = (r)oot of galaxy web server (/home/galaxyuser/galaxy-dist)
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22 # H = (H)ost of the galaxy web server (http://my.galaxy.server/galaxy/)
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23 getopts('v:u:n:a:g:o:b:B:V:c:S:R:H:', \%opts); # option are in %opts
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24
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25
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26 #################
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27 ## CHECK INPUT ##
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28 #################
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29 if (!exists($opts{'v'})) {
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30 die('No VCF File Specified');
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31 }
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32 if (!-e $opts{'v'}) {
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33 die('VCF File not found');
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34 }
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35 if (!exists($opts{'u'})) {
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36 die('No user specified');
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37 }
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38 if (!exists($opts{'S'})) {
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39 die('No VariantDB server specified');
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40 }
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41 if (!exists($opts{'H'})) {
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42 die('The Galaxy source-server is not specified');
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43 }
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44
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45 ################
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46 # open outfile #
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47 ################
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48 open OUT, ">$opts{'o'}";
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49
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50 ###############################
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51 ## TEST CONNECTION TO SERVER ##
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52 ###############################
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53 use LWP::UserAgent;
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54 my $url = $opts{'S'}."/";
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55 $url =~ s/\/\/$/\//;
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56 $url .= "cgi-bin/galaxy_communication.cgi";
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57 my $conn = LWP::UserAgent->new();
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58 my $response = $conn->post( $url, {'HelloWorld' => 1} );
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59 my $content = $response->decoded_content();
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60
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61 if ($content eq 'HelloGalaxy') {
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62 print OUT "Testing connection to $opts{'S'} : OK.\n";
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63 }
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64 else {
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65 die("Could not connect to the specified server : $content");
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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 ## TEST USER ID ##
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71 ##################
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72 $email = $opts{'u'};
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73 my $response = $conn->post( $url, {'CheckUser' => $email} );
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74 my $content = $response->decoded_content();
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75
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76 if ($content eq 'OK') {
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77 print OUT "Testing User-existence : OK.\n";
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78 }
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79 else {
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80 die("ERROR: $content");
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81 }
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82
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83 ###############################################
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84 ## SEND THE VCF AND BAM FILES FOR PROCESSING ##
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85 ###############################################
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86 # filepaths
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87 my $vcfpath = $opts{'v'};
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88 my $bampath = $opts{'b'};
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89 my $baipath = $opts{'B'};
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90 # make output directory in (galaxy/static/) working dir
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91 my $rand = int(rand(1000));
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92 our $wd = $opts{'R'}."/static/VCF_parser.".$rand; #int(rand(1000));
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93 our $dd = $opts{'H'}."/static/VCF_parser.".$rand;
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94 while (-d $wd) {
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95 my $rand = int(rand(1000));
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96 $wd = $opts{'R'}."/static/VCF_parser.".$rand;#int(rand(1000));
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97 $dd = $opts{'H'}."/static/VCF_parser.".$rand;
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98
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99 }
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100 $result = system("mkdir $wd");
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101
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102
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103 ## link files
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104 $vcfurl = "$dd/data.vcf";
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105 system ("ln -s $vcfpath $wd/data.vcf");
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106 if (exists($opts{'b'})) {
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107 $bamurl = "$dd/data.bam";
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108 $bamidxurl = "$dd/data.bai";
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109 system ("ln -s $bampath $wd/data.bam");
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110 system ("ln -s $baipath $wd/data.bai");
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111 }
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112 $sample = $opts{'n'};
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113 $gender = $opts{'g'};
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114 # post form to the variantDB host.
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115 if (exists($opts{'b'})) {
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116 $response = $conn->post( $url, {'VCFurl1' => "$vcfurl", 'BAMurl1' => "$bamurl", 'BAIurl1' => "$bamidxurl",'storedata' => 1, 'name1' => "$sample", 'gender1' => "$gender", 'User' => $email} );
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117 }
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118 else {
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119 $response = $conn->post( $url, {'VCFurl1' => "$vcfurl", 'sample1' => "$sample", 'gender1' => "$gender", 'User' => $email} );
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120 }
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121 my $content = $response->decoded_content();
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122 chomp($content);
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123 if ($content =~ m/OK$/) {
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124 print OUT "Processing Datafiles : OK.\n";
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125 print OUT "\n$content\n";
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126 }
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127 else {
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128 die("ERROR: $content");
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129 }
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130 close OUT;
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131
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132 # clean up
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133 system("rm -Rf '$wd'");
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134
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