Mercurial > repos > geert-vandeweyer > vcf_to_variantdb
annotate VCF_to_VariantDB.pl @ 8:db44ff975de8 draft
Corrected macro.xml handling of GALAXY_URL
| author | geert-vandeweyer |
|---|---|
| date | Tue, 10 Jun 2014 06:01:18 -0400 |
| parents | 04e3bba317f4 |
| children | 3b27cae9b359 |
| rev | line source |
|---|---|
| 1 | 1 #!/usr/bin/perl |
| 2 | |
| 3 # load modules | |
| 4 use Getopt::Std; | |
| 5 | |
| 6 ########################## | |
| 7 # COMMAND LINE ARGUMENTS # | |
| 8 ########################## | |
| 9 # v = (v)cf file to load | |
| 10 # V = (V)CF file encoded id | |
| 11 # u = (u)ser email from galaxy | |
| 12 # n = sample (n)ame | |
| 13 # a = sample (a)nnotation | |
| 14 # g = sample (g)ender | |
| 15 # o = (o)utput file (simple text file) | |
| 16 # b = (b)am file (optional) | |
| 17 # B = (B)am index , needed if b is specified | |
| 18 # c = encoded id of bam file (optional) | |
| 19 # C = encoded id of Bam index , needed if b is specified => NOT POSSIBLE YET, NEEDS INDEXING ON VARIANTDB SERVER ! | |
| 20 # S = (S)erver addrress to send data to. | |
| 21 # R = (r)oot of galaxy web server (/home/galaxyuser/galaxy-dist) | |
| 22 # H = (H)ost of the galaxy web server (http://my.galaxy.server/galaxy/) | |
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23 # F = (F)ormat of input file |
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24 getopts('v:u:n:a:g:o:b:B:V:c:S:R:H:F:', \%opts); # option are in %opts |
| 1 | 25 |
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26 $|++; |
| 1 | 27 ################# |
| 28 ## CHECK INPUT ## | |
| 29 ################# | |
| 30 if (!exists($opts{'v'})) { | |
| 31 die('No VCF File Specified'); | |
| 32 } | |
| 33 if (!-e $opts{'v'}) { | |
| 34 die('VCF File not found'); | |
| 35 } | |
| 36 if (!exists($opts{'u'})) { | |
| 37 die('No user specified'); | |
| 38 } | |
| 39 if (!exists($opts{'S'})) { | |
| 40 die('No VariantDB server specified'); | |
| 41 } | |
| 42 if (!exists($opts{'H'})) { | |
| 43 die('The Galaxy source-server is not specified'); | |
| 44 } | |
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45 if (!exists($opts{'F'})) { |
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46 die('VCF format not specified.'); |
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47 } |
| 1 | 48 |
| 49 ################ | |
| 50 # open outfile # | |
| 51 ################ | |
| 52 open OUT, ">$opts{'o'}"; | |
| 53 | |
| 54 ############################### | |
| 55 ## TEST CONNECTION TO SERVER ## | |
| 56 ############################### | |
| 57 use LWP::UserAgent; | |
| 58 my $url = $opts{'S'}."/"; | |
| 59 $url =~ s/\/\/$/\//; | |
| 60 $url .= "cgi-bin/galaxy_communication.cgi"; | |
| 61 my $conn = LWP::UserAgent->new(); | |
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62 $conn->timeout(1800); |
| 1 | 63 my $response = $conn->post( $url, {'HelloWorld' => 1} ); |
| 64 my $content = $response->decoded_content(); | |
| 65 | |
| 66 if ($content eq 'HelloGalaxy') { | |
| 67 print OUT "Testing connection to $opts{'S'} : OK.\n"; | |
| 68 } | |
| 69 else { | |
| 70 die("Could not connect to the specified server : $content"); | |
| 71 } | |
| 72 | |
| 73 | |
| 74 ################## | |
| 75 ## TEST USER ID ## | |
| 76 ################## | |
| 77 $email = $opts{'u'}; | |
| 78 my $response = $conn->post( $url, {'CheckUser' => $email} ); | |
| 79 my $content = $response->decoded_content(); | |
| 80 | |
| 81 if ($content eq 'OK') { | |
| 82 print OUT "Testing User-existence : OK.\n"; | |
| 83 } | |
| 84 else { | |
| 85 die("ERROR: $content"); | |
| 86 } | |
| 87 | |
| 5 | 88 print $opts{'H'}. " was specified as galaxy host\n"; |
| 89 | |
| 1 | 90 ############################################### |
| 91 ## SEND THE VCF AND BAM FILES FOR PROCESSING ## | |
| 92 ############################################### | |
| 93 # filepaths | |
| 94 my $vcfpath = $opts{'v'}; | |
| 95 my $bampath = $opts{'b'}; | |
| 96 my $baipath = $opts{'B'}; | |
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97 # input VCF format |
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98 $format = $opts{'F'}; |
| 1 | 99 # make output directory in (galaxy/static/) working dir |
| 100 my $rand = int(rand(1000)); | |
| 101 our $wd = $opts{'R'}."/static/VCF_parser.".$rand; #int(rand(1000)); | |
| 102 our $dd = $opts{'H'}."/static/VCF_parser.".$rand; | |
| 103 while (-d $wd) { | |
| 104 my $rand = int(rand(1000)); | |
| 105 $wd = $opts{'R'}."/static/VCF_parser.".$rand;#int(rand(1000)); | |
| 106 $dd = $opts{'H'}."/static/VCF_parser.".$rand; | |
| 107 | |
| 108 } | |
| 109 $result = system("mkdir $wd"); | |
| 110 | |
| 111 | |
| 112 ## link files | |
| 113 $vcfurl = "$dd/data.vcf"; | |
| 8 | 114 $vcfurl =~ s/\s//g; |
| 1 | 115 system ("ln -s $vcfpath $wd/data.vcf"); |
| 116 if (exists($opts{'b'})) { | |
| 117 $bamurl = "$dd/data.bam"; | |
| 8 | 118 $bamurl =~ s/\s//g; |
| 1 | 119 $bamidxurl = "$dd/data.bai"; |
| 8 | 120 $bamidxurl =~ s/\s//g; |
| 1 | 121 system ("ln -s $bampath $wd/data.bam"); |
| 122 system ("ln -s $baipath $wd/data.bai"); | |
| 123 } | |
| 124 $sample = $opts{'n'}; | |
| 125 $gender = $opts{'g'}; | |
| 126 # post form to the variantDB host. | |
| 127 if (exists($opts{'b'})) { | |
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128 $response = $conn->post( $url, {'VCFurl1' => "$vcfurl", 'BAMurl1' => "$bamurl", 'BAIurl1' => "$bamidxurl",'storedata1' => 1, 'name1' => "$sample", 'gender1' => "$gender", 'User' => $email, 'GalaxyUpload' => 1,'Format1' => $format} ); |
| 1 | 129 } |
| 130 else { | |
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131 $response = $conn->post( $url, {'VCFurl1' => "$vcfurl", 'name1' => "$sample", 'gender1' => "$gender", 'User' => $email, 'GalaxyUpload' =>1, 'Format1' => $format } ); |
| 1 | 132 } |
| 133 my $content = $response->decoded_content(); | |
| 134 chomp($content); | |
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135 ## check if upload went ok. |
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136 if (substr($content,0,2) ne 'OK') { |
| 1 | 137 die("ERROR: $content"); |
| 138 } | |
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139 ## extract wd from content. |
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140 print OUT "Uploading datafiles to VariantDB : OK.\n"; |
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141 $content =~ m/OK-(.+)$/; |
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142 $rwd = $1; |
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143 if ($rwd eq '') { |
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144 die("ERROR : No remote working directory provided to check status."); |
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145 } |
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146 ## now wait for the import to finish. |
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147 $status = 0; |
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148 while ($status == 0) { |
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149 my $response = $conn->post( $url, {'CheckStatus' => 1,'rwd' => $rwd}) ; |
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150 $content = $response->decoded_content(); |
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151 chomp($content); |
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152 if (substr($content,0,2) ne 'OK') { |
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153 die("ERROR: $content"); |
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154 } |
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155 $status = substr($content,3,1); |
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156 sleep 10; |
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157 } |
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158 |
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159 ## Loading OK |
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160 # latest respons : OK-1-Content |
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161 $content = substr($content,5); |
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162 print OUT "Processing Datafiles : OK.\n"; |
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163 print OUT "\n$content\n"; |
| 1 | 164 close OUT; |
| 165 | |
| 166 # clean up | |
| 167 system("rm -Rf '$wd'"); | |
| 168 |