Mercurial > repos > geert-vandeweyer > vcf_to_variantdb

comparison VCF_to_VariantDB.pl @ 7:04e3bba317f4 draft

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Added selection to differentiate in VCF format
author geert-vandeweyer
date Thu, 05 Jun 2014 04:02:28 -0400
parents 6ddc1c6472ef
children db44ff975de8
comparison
equal deleted inserted replaced
6:775372e00f55 7:04e3bba317f4
18 # c = encoded id of bam file (optional) 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 ! 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. 20 # S = (S)erver addrress to send data to.
21 # R = (r)oot of galaxy web server (/home/galaxyuser/galaxy-dist) 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/) 22 # H = (H)ost of the galaxy web server (http://my.galaxy.server/galaxy/)
23 getopts('v:u:n:a:g:o:b:B:V:c:S:R:H:', \%opts); # option are in %opts 23 # F = (F)ormat of input file
24 getopts('v:u:n:a:g:o:b:B:V:c:S:R:H:F:', \%opts); # option are in %opts
24 25
25 $|++; 26 $|++;
26 ################# 27 #################
27 ## CHECK INPUT ## 28 ## CHECK INPUT ##
28 ################# 29 #################
38 if (!exists($opts{'S'})) { 39 if (!exists($opts{'S'})) {
39 die('No VariantDB server specified'); 40 die('No VariantDB server specified');
40 } 41 }
41 if (!exists($opts{'H'})) { 42 if (!exists($opts{'H'})) {
42 die('The Galaxy source-server is not specified'); 43 die('The Galaxy source-server is not specified');
44 }
45 if (!exists($opts{'F'})) {
46 die('VCF format not specified.');
43 } 47 }
44 48
45 ################ 49 ################
46 # open outfile # 50 # open outfile #
47 ################ 51 ################
88 ############################################### 92 ###############################################
89 # filepaths 93 # filepaths
90 my $vcfpath = $opts{'v'}; 94 my $vcfpath = $opts{'v'};
91 my $bampath = $opts{'b'}; 95 my $bampath = $opts{'b'};
92 my $baipath = $opts{'B'}; 96 my $baipath = $opts{'B'};
97 # input VCF format
98 $format = $opts{'F'};
93 # make output directory in (galaxy/static/) working dir 99 # make output directory in (galaxy/static/) working dir
94 my $rand = int(rand(1000)); 100 my $rand = int(rand(1000));
95 our $wd = $opts{'R'}."/static/VCF_parser.".$rand; #int(rand(1000)); 101 our $wd = $opts{'R'}."/static/VCF_parser.".$rand; #int(rand(1000));
96 our $dd = $opts{'H'}."/static/VCF_parser.".$rand; 102 our $dd = $opts{'H'}."/static/VCF_parser.".$rand;
97 while (-d $wd) { 103 while (-d $wd) {
114 } 120 }
115 $sample = $opts{'n'}; 121 $sample = $opts{'n'};
116 $gender = $opts{'g'}; 122 $gender = $opts{'g'};
117 # post form to the variantDB host. 123 # post form to the variantDB host.
118 if (exists($opts{'b'})) { 124 if (exists($opts{'b'})) {
119 $response = $conn->post( $url, {'VCFurl1' => "$vcfurl", 'BAMurl1' => "$bamurl", 'BAIurl1' => "$bamidxurl",'storedata1' => 1, 'name1' => "$sample", 'gender1' => "$gender", 'User' => $email, 'GalaxyUpload' => 1} ); 125 $response = $conn->post( $url, {'VCFurl1' => "$vcfurl", 'BAMurl1' => "$bamurl", 'BAIurl1' => "$bamidxurl",'storedata1' => 1, 'name1' => "$sample", 'gender1' => "$gender", 'User' => $email, 'GalaxyUpload' => 1,'Format1' => $format} );
120 } 126 }
121 else { 127 else {
122 $response = $conn->post( $url, {'VCFurl1' => "$vcfurl", 'name1' => "$sample", 'gender1' => "$gender", 'User' => $email, 'GalaxyUpload' =>1 } ); 128 $response = $conn->post( $url, {'VCFurl1' => "$vcfurl", 'name1' => "$sample", 'gender1' => "$gender", 'User' => $email, 'GalaxyUpload' =>1, 'Format1' => $format } );
123 } 129 }
124 my $content = $response->decoded_content(); 130 my $content = $response->decoded_content();
125 chomp($content); 131 chomp($content);
126 ## check if upload went ok. 132 ## check if upload went ok.
127 if (substr($content,0,2) ne 'OK') { 133 if (substr($content,0,2) ne 'OK') {