Mercurial > repos > geert-vandeweyer > vcf_to_variantdb

comparison VCF_to_VariantDB.pl @ 1:355e491dbd0f draft

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author geert-vandeweyer
date Wed, 08 May 2013 04:34:30 -0400
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children d03a63a57e82
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0:156964ba18fc 1:355e491dbd0f
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/)
23 getopts('v:u:n:a:g:o:b:B:V:c:S:R:H:', \%opts); # option are in %opts
24
25
26 #################
27 ## CHECK INPUT ##
28 #################
29 if (!exists($opts{'v'})) {
30 die('No VCF File Specified');
31 }
32 if (!-e $opts{'v'}) {
33 die('VCF File not found');
34 }
35 if (!exists($opts{'u'})) {
36 die('No user specified');
37 }
38 if (!exists($opts{'S'})) {
39 die('No VariantDB server specified');
40 }
41 if (!exists($opts{'H'})) {
42 die('The Galaxy source-server is not specified');
43 }
44
45 ################
46 # open outfile #
47 ################
48 open OUT, ">$opts{'o'}";
49
50 ###############################
51 ## TEST CONNECTION TO SERVER ##
52 ###############################
53 use LWP::UserAgent;
54 my $url = $opts{'S'}."/";
55 $url =~ s/\/\/$/\//;
56 $url .= "cgi-bin/galaxy_communication.cgi";
57 my $conn = LWP::UserAgent->new();
58 my $response = $conn->post( $url, {'HelloWorld' => 1} );
59 my $content = $response->decoded_content();
60
61 if ($content eq 'HelloGalaxy') {
62 print OUT "Testing connection to $opts{'S'} : OK.\n";
63 }
64 else {
65 die("Could not connect to the specified server : $content");
66 }
67
68
69 ##################
70 ## TEST USER ID ##
71 ##################
72 $email = $opts{'u'};
73 my $response = $conn->post( $url, {'CheckUser' => $email} );
74 my $content = $response->decoded_content();
75
76 if ($content eq 'OK') {
77 print OUT "Testing User-existence : OK.\n";
78 }
79 else {
80 die("ERROR: $content");
81 }
82
83 ###############################################
84 ## SEND THE VCF AND BAM FILES FOR PROCESSING ##
85 ###############################################
86 # filepaths
87 my $vcfpath = $opts{'v'};
88 my $bampath = $opts{'b'};
89 my $baipath = $opts{'B'};
90 # make output directory in (galaxy/static/) working dir
91 my $rand = int(rand(1000));
92 our $wd = $opts{'R'}."/static/VCF_parser.".$rand; #int(rand(1000));
93 our $dd = $opts{'H'}."/static/VCF_parser.".$rand;
94 while (-d $wd) {
95 my $rand = int(rand(1000));
96 $wd = $opts{'R'}."/static/VCF_parser.".$rand;#int(rand(1000));
97 $dd = $opts{'H'}."/static/VCF_parser.".$rand;
98
99 }
100 $result = system("mkdir $wd");
101
102
103 ## link files
104 $vcfurl = "$dd/data.vcf";
105 system ("ln -s $vcfpath $wd/data.vcf");
106 if (exists($opts{'b'})) {
107 $bamurl = "$dd/data.bam";
108 $bamidxurl = "$dd/data.bai";
109 system ("ln -s $bampath $wd/data.bam");
110 system ("ln -s $baipath $wd/data.bai");
111 }
112 $sample = $opts{'n'};
113 $gender = $opts{'g'};
114 # post form to the variantDB host.
115 if (exists($opts{'b'})) {
116 $response = $conn->post( $url, {'VCFurl1' => "$vcfurl", 'BAMurl1' => "$bamurl", 'BAIurl1' => "$bamidxurl",'storedata' => 1, 'name1' => "$sample", 'gender1' => "$gender", 'User' => $email} );
117 }
118 else {
119 $response = $conn->post( $url, {'VCFurl1' => "$vcfurl", 'sample1' => "$sample", 'gender1' => "$gender", 'User' => $email} );
120 }
121 my $content = $response->decoded_content();
122 chomp($content);
123 if ($content =~ m/OK$/) {
124 print OUT "Processing Datafiles : OK.\n";
125 print OUT "\n$content\n";
126 }
127 else {
128 die("ERROR: $content");
129 }
130 close OUT;
131
132 # clean up
133 system("rm -Rf '$wd'");
134