CORDEA / 1000genomes-visualization

1000 Genomes Visualization

The repository contains a program of Web services using the SNP data of 1000 Genomes Project.

Features

• focused on the difference of Genotype frequency by Ethnicity.

Use library

• Python
  • Flask
  • MySQL.connector
• JavaScript
  • jQuery
  • jVectorMap
  • Highcharts

Version (recommended)

• python 2.7.5
• flask 0.10.1
• MySQL.connector 1.2.2
• jQuery 1.11.0
• jVectorMap 1.2.2

DataBase

OverView

• Engine : InnoDB
• Size : 25.2GiB
• Column : 85,639,460
• Encoding: utf-8

Table design

CREATE TABLE `main` (
  `chr` varchar(2) NOT NULL DEFAULT '',
  `pos` int(15) NOT NULL,
  `id` varchar(15) NOT NULL,
  `REF` tinytext NOT NULL,
  `ALT` tinytext NOT NULL,
  `info` text NOT NULL,
  KEY `id` (`id`),
  KEY `pos` (`pos`)
) ENGINE=InnoDB DEFAULT CHARSET=utf8;

Example

Column	Content
chr	1
pos	10177
id	.
REF	A
ALT	AC
info	1|1:23,1|0:29,0|1:28,0|0:33;1|1:9,0|1:34,1|0:20,0|0:31;1|1:28,0|1:15,1|0:27,0|0:16;0|0:19,0|1:30,1|0:26,1|1:10;1|1:9,1|0:37,0|1:36,0|0:17;1|1:35,0|1:19,1|0:24,0|0:7;1|1:3,0|1:21,1|0:31,0|0:36;0|0:34,1|0:23,0|1:42,1|1:8;1|1:2,0|1:15,1|0:23,0|0:21;1|1:4,0|1:26,1|0:24,0|0:45;1|1:21,0|1:39,1|0:42,0|0:5;0|0:38,0|1:28,1|0:29,1|1:4;1|1:7,1|0:36,0|1:38,0|0:18;0|0:13,0|1:43,1|0:41,1|1:11;1|1:1,0|1:38,1|0:30,0|0:34;0|0:16,1|0:30,0|1:36,1|1:20;1|0:21,0|1:22,0|0:62;1|1:30,0|1:26,1|0:28,0|0:15;1|1:12,0|1:26,1|0:30,0|0:28;0|0:19,0|1:24,1|0:40,1|1:20;1|1:8,1|0:26,0|1:28,0|0:34;1|0:19,0|1:20,0|0:25;1|1:18,1|0:32,0|1:38,0|0:14;1|1:10,1|0:16,0|1:13,0|0:54;0|0:13,1|0:40,0|1:30,1|1:21;1|1:6,0|1:24,1|0:27,0|0:47

License

Copyright 2014-2016 Yoshihiro Tanaka

Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at

    http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.