comparison VCF_to_VariantDB.pl @ 7:04e3bba317f4 draft

Added selection to differentiate in VCF format

6:775372e00f55

# c = encoded id of bam file (optional)
# C = encoded id of Bam index , needed if b is specified => NOT POSSIBLE YET, NEEDS INDEXING ON VARIANTDB SERVER !
# S = (S)erver addrress to send data to.
# R = (r)oot of galaxy web server (/home/galaxyuser/galaxy-dist)
# H = (H)ost of the galaxy web server (http://my.galaxy.server/galaxy/)
getopts('v:u:n:a:g:o:b:B:V:c:S:R:H:', \%opts);  # option are in %opts

$|++;
#################
## CHECK INPUT ##
#################

if (!exists($opts{'S'})) {
	die('No VariantDB server specified');
}
if (!exists($opts{'H'})) {
	die('The Galaxy source-server is not specified');
}

################
# open outfile #
################

###############################################
# filepaths
my $vcfpath = $opts{'v'};
my $bampath = $opts{'b'};
my $baipath = $opts{'B'};
# make output directory in (galaxy/static/) working dir
my $rand = int(rand(1000));
our $wd = $opts{'R'}."/static/VCF_parser.".$rand; #int(rand(1000));
our $dd = $opts{'H'}."/static/VCF_parser.".$rand;
while (-d $wd) {

}	
$sample = $opts{'n'};
$gender = $opts{'g'};
# post form to the variantDB host. 
if (exists($opts{'b'})) {
	$response = $conn->post( $url, {'VCFurl1' => "$vcfurl", 'BAMurl1' => "$bamurl", 'BAIurl1' => "$bamidxurl",'storedata1' => 1, 'name1' => "$sample", 'gender1' => "$gender", 'User' => $email, 'GalaxyUpload' => 1} );
}
else {
	$response = $conn->post( $url, {'VCFurl1' => "$vcfurl",  'name1' => "$sample", 'gender1' => "$gender", 'User' => $email, 'GalaxyUpload' =>1 } );
}
my $content = $response->decoded_content();
chomp($content);
## check if upload went ok.
if (substr($content,0,2) ne 'OK') {

7:04e3bba317f4

# c = encoded id of bam file (optional)
# C = encoded id of Bam index , needed if b is specified => NOT POSSIBLE YET, NEEDS INDEXING ON VARIANTDB SERVER !
# S = (S)erver addrress to send data to.
# R = (r)oot of galaxy web server (/home/galaxyuser/galaxy-dist)
# H = (H)ost of the galaxy web server (http://my.galaxy.server/galaxy/)
# F = (F)ormat of input file 
getopts('v:u:n:a:g:o:b:B:V:c:S:R:H:F:', \%opts);  # option are in %opts

$|++;
#################
## CHECK INPUT ##
#################

if (!exists($opts{'S'})) {
	die('No VariantDB server specified');
}
if (!exists($opts{'H'})) {
	die('The Galaxy source-server is not specified');
}
if (!exists($opts{'F'})) {
	die('VCF format not specified.');
}

################
# open outfile #
################

###############################################
# filepaths
my $vcfpath = $opts{'v'};
my $bampath = $opts{'b'};
my $baipath = $opts{'B'};
# input VCF format
$format = $opts{'F'};
# make output directory in (galaxy/static/) working dir
my $rand = int(rand(1000));
our $wd = $opts{'R'}."/static/VCF_parser.".$rand; #int(rand(1000));
our $dd = $opts{'H'}."/static/VCF_parser.".$rand;
while (-d $wd) {

}	
$sample = $opts{'n'};
$gender = $opts{'g'};
# post form to the variantDB host. 
if (exists($opts{'b'})) {
	$response = $conn->post( $url, {'VCFurl1' => "$vcfurl", 'BAMurl1' => "$bamurl", 'BAIurl1' => "$bamidxurl",'storedata1' => 1, 'name1' => "$sample", 'gender1' => "$gender", 'User' => $email, 'GalaxyUpload' => 1,'Format1' => $format} );
}
else {
	$response = $conn->post( $url, {'VCFurl1' => "$vcfurl",  'name1' => "$sample", 'gender1' => "$gender", 'User' => $email, 'GalaxyUpload' =>1, 'Format1' => $format } );
}
my $content = $response->decoded_content();
chomp($content);
## check if upload went ok.
if (substr($content,0,2) ne 'OK') {