This page is offering some sample scripts to you effective for the data processing of Illumina 1M-Duo. It is useful to make huge data of genotype and/or phenotype with PAGE-OM standard format.
dbSNP is operating on MS SQLServer. Moreover, only the script for SQLServer is being offered. Then, This page offers the script that can be used on MySQL.
These scripts help you to create phenotype tables.
Example of script: create table tbl_page_phenotype.sql
create table tbl_page_phenotype ( height varchar(20), weight varchar(20), BMI varchar(20), systolic_blood_pressure varchar(20), diastolic_blood_pressure varchar(20), ECG varchar(20), HR varchar(20), protein varchar(20), albumin varchar(20), bilirubin varchar(20), AST_GOT varchar(20), ALT_GPT varchar(20), LDH_JSCC varchar(20), G-GTP_JSCC varchar(20), ALP_JSCC varchar(20), CRP varchar(20), total_cholesterol varchar(20), TG varchar(20), phospholoid varchar(20), urinary_nitrogen varchar(20), creatinine varchar(20), UA_uric_aid varchar(20), HbA1c varchar(20), Na varchar(20), Cl varchar(20), Ka varchar(20), Ca varchar(20), HBS_antigen varchar(20), HCV_antibody_RIA varchar(20), HCV_antibody_RIA_decision varchar(20), HCV_antibody_RIA_index varchar(20), WBC_count varchar(20), RBC_count varchar(20) ) ; |
This sample Perl script helps you to extract data from MySQL by an example. The user table is necessary to execute it appropriately.
Example of script: makexml_gv_full.pl
#!usr/bin/perl
#########################
# xmlmake_gv_full.pl
#
use DBI;
$ds = 'DBI:mysql:pageomdb;host=localhost;port=3306';
$user = 'pageom';
$pass = 'pageompassxxxx';
$string = 'rs112078';
$db = DBI->connect($ds, $user, $pass) || die "Got error $DBI::errstr when connecting to $ds\n";
# for test
$sth = $db->prepare("select * from tbl_array WHERE rsname like \'$string\%\' and subsnp_id is not null");
# real thing
#$sth = $db->prepare("select * from tbl_array WHERE subsnp_id is not null");
$sth->execute;
#print "Content-type: text/html;\n\n";
while(@row = $sth->fetchrow_array) {
# for debug
# print "@row\n";
# print $row[0] . "\n";
# print $row[1] . "\n";
# print $row[2] . "\n";
print "\t
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