first commit

Dockerfile

@@ -0,0 +1,47 @@
+FROM ubuntu:14.04
+MAINTAINER Chanaka Mannapperuma <irusri@yahoo.com>
+
+# Setup environment
+ENV DEBIAN_FRONTEND noninteractive
+
+# Update sources
+RUN apt-get update -y
+
+# install http
+RUN apt-get install -y apache2 vim bash-completion unzip
+RUN mkdir -p /var/lock/apache2 /var/run/apache2
+
+# install mysql
+RUN apt-get install -y mysql-client mysql-server
+#RUN echo "NETWORKING=yes" > /etc/sysconfig/network
+# start mysqld to create initial tables
+#RUN service mysqld start
+
+# install php
+RUN apt-get install -y php5 php5-mysql php5-dev php5-gd php5-memcache php5-pspell php5-snmp snmp php5-xmlrpc libapache2-mod-php5 php5-cli
+#RUN yum install -y php php-mysql php-devel php-gd php-pecl-memcache php-pspell php-snmp php-xmlrpc php-xml
+
+# install supervisord
+
+RUN apt-get install -y supervisor
+RUN mkdir -p /var/log/supervisor
+
+
+# install sshd
+RUN apt-get install -y openssh-server openssh-client passwd
+RUN mkdir -p /var/run/sshd
+
+#RUN ssh-keygen -q -N "" -t dsa -f /etc/ssh/ssh_host_dsa_key && ssh-keygen -q -N "" -t rsa -f /etc/ssh/ssh_host_rsa_key 
+RUN sed -ri 's/PermitRootLogin without-password/PermitRootLogin yes/g' /etc/ssh/sshd_config
+RUN echo 'root:changeme' | chpasswd
+
+# Put your own public key at id_rsa.pub for key-based login.
+RUN mkdir -p /root/.ssh && touch /root/.ssh/authorized_keys && chmod 700 /root/.ssh
+#ADD id_rsa.pub /root/.ssh/authorized_keys
+
+
+#ADD genie /var/www/html/
+ADD supervisord.conf /etc/
+EXPOSE 22 80 443
+
+CMD ["supervisord", "-n"]

LICENSE

@@ -0,0 +1,165 @@
+                   GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+
+  This version of the GNU Lesser General Public License incorporates
+the terms and conditions of version 3 of the GNU General Public
+License, supplemented by the additional permissions listed below.
+
+  0. Additional Definitions.
+
+  As used herein, "this License" refers to version 3 of the GNU Lesser
+General Public License, and the "GNU GPL" refers to version 3 of the GNU
+General Public License.
+
+  "The Library" refers to a covered work governed by this License,
+other than an Application or a Combined Work as defined below.
+
+  An "Application" is any work that makes use of an interface provided
+by the Library, but which is not otherwise based on the Library.
+Defining a subclass of a class defined by the Library is deemed a mode
+of using an interface provided by the Library.
+
+  A "Combined Work" is a work produced by combining or linking an
+Application with the Library.  The particular version of the Library
+with which the Combined Work was made is also called the "Linked
+Version".
+
+  The "Minimal Corresponding Source" for a Combined Work means the
+Corresponding Source for the Combined Work, excluding any source code
+for portions of the Combined Work that, considered in isolation, are
+based on the Application, and not on the Linked Version.
+
+  The "Corresponding Application Code" for a Combined Work means the
+object code and/or source code for the Application, including any data
+and utility programs needed for reproducing the Combined Work from the
+Application, but excluding the System Libraries of the Combined Work.
+
+  1. Exception to Section 3 of the GNU GPL.
+
+  You may convey a covered work under sections 3 and 4 of this License
+without being bound by section 3 of the GNU GPL.
+
+  2. Conveying Modified Versions.
+
+  If you modify a copy of the Library, and, in your modifications, a
+facility refers to a function or data to be supplied by an Application
+that uses the facility (other than as an argument passed when the
+facility is invoked), then you may convey a copy of the modified
+version:
+
+   a) under this License, provided that you make a good faith effort to
+   ensure that, in the event an Application does not supply the
+   function or data, the facility still operates, and performs
+   whatever part of its purpose remains meaningful, or
+
+   b) under the GNU GPL, with none of the additional permissions of
+   this License applicable to that copy.
+
+  3. Object Code Incorporating Material from Library Header Files.
+
+  The object code form of an Application may incorporate material from
+a header file that is part of the Library.  You may convey such object
+code under terms of your choice, provided that, if the incorporated
+material is not limited to numerical parameters, data structure
+layouts and accessors, or small macros, inline functions and templates
+(ten or fewer lines in length), you do both of the following:
+
+   a) Give prominent notice with each copy of the object code that the
+   Library is used in it and that the Library and its use are
+   covered by this License.
+
+   b) Accompany the object code with a copy of the GNU GPL and this license
+   document.
+
+  4. Combined Works.
+
+  You may convey a Combined Work under terms of your choice that,
+taken together, effectively do not restrict modification of the
+portions of the Library contained in the Combined Work and reverse
+engineering for debugging such modifications, if you also do each of
+the following:
+
+   a) Give prominent notice with each copy of the Combined Work that
+   the Library is used in it and that the Library and its use are
+   covered by this License.
+
+   b) Accompany the Combined Work with a copy of the GNU GPL and this license
+   document.
+
+   c) For a Combined Work that displays copyright notices during
+   execution, include the copyright notice for the Library among
+   these notices, as well as a reference directing the user to the
+   copies of the GNU GPL and this license document.
+
+   d) Do one of the following:
+
+       0) Convey the Minimal Corresponding Source under the terms of this
+       License, and the Corresponding Application Code in a form
+       suitable for, and under terms that permit, the user to
+       recombine or relink the Application with a modified version of
+       the Linked Version to produce a modified Combined Work, in the
+       manner specified by section 6 of the GNU GPL for conveying
+       Corresponding Source.
+
+       1) Use a suitable shared library mechanism for linking with the
+       Library.  A suitable mechanism is one that (a) uses at run time
+       a copy of the Library already present on the user's computer
+       system, and (b) will operate properly with a modified version
+       of the Library that is interface-compatible with the Linked
+       Version.
+
+   e) Provide Installation Information, but only if you would otherwise
+   be required to provide such information under section 6 of the
+   GNU GPL, and only to the extent that such information is
+   necessary to install and execute a modified version of the
+   Combined Work produced by recombining or relinking the
+   Application with a modified version of the Linked Version. (If
+   you use option 4d0, the Installation Information must accompany
+   the Minimal Corresponding Source and Corresponding Application
+   Code. If you use option 4d1, you must provide the Installation
+   Information in the manner specified by section 6 of the GNU GPL
+   for conveying Corresponding Source.)
+
+  5. Combined Libraries.
+
+  You may place library facilities that are a work based on the
+Library side by side in a single library together with other library
+facilities that are not Applications and are not covered by this
+License, and convey such a combined library under terms of your
+choice, if you do both of the following:
+
+   a) Accompany the combined library with a copy of the same work based
+   on the Library, uncombined with any other library facilities,
+   conveyed under the terms of this License.
+
+   b) Give prominent notice with the combined library that part of it
+   is a work based on the Library, and explaining where to find the
+   accompanying uncombined form of the same work.
+
+  6. Revised Versions of the GNU Lesser General Public License.
+
+  The Free Software Foundation may publish revised and/or new versions
+of the GNU Lesser General Public License from time to time. Such new
+versions will be similar in spirit to the present version, but may
+differ in detail to address new problems or concerns.
+
+  Each version is given a distinguishing version number. If the
+Library as you received it specifies that a certain numbered version
+of the GNU Lesser General Public License "or any later version"
+applies to it, you have the option of following the terms and
+conditions either of that published version or of any later version
+published by the Free Software Foundation. If the Library as you
+received it does not specify a version number of the GNU Lesser
+General Public License, you may choose any version of the GNU Lesser
+General Public License ever published by the Free Software Foundation.
+
+  If the Library as you received it specifies that a proxy can decide
+whether future versions of the GNU Lesser General Public License shall
+apply, that proxy's public statement of acceptance of any version is
+permanent authorization for you to choose that version for the
+Library.

README.md

@@ -0,0 +1,2 @@
+# scripts
+Data preparation and loading scripts for GenIE-CMS

biomart_download.sh

@@ -0,0 +1,4 @@
+#!/bin/bash
+
+BM=`sed ':a;N;$!ba;s/\n/ /g' xml/$1`
+wget -O ../output/$1.tab "https://phytozome.jgi.doe.gov/biomart/martservice?query=$BM"

dump.sql

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+SET NAMES utf8;
+SET FOREIGN_KEY_CHECKS = 0;
+
+-- ----------------------------
+--  Table structure for `correlation_expatlas_clr`
+-- ----------------------------
+DROP TABLE IF EXISTS `correlation_expatlas_clr`;
+CREATE TABLE `correlation_expatlas_clr` (
+  `edg_id` int(11) unsigned NOT NULL AUTO_INCREMENT,
+  `gene_i1` int(11) NOT NULL,
+  `gene_i2` int(11) NOT NULL,
+  `corr1` double(16,10) DEFAULT NULL,
+  PRIMARY KEY (`edg_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 AUTO_INCREMENT=1;
+
+-- ----------------------------
+--  Table structure for `expression_exatlas_tissue_tpm`
+-- ----------------------------
+DROP TABLE IF EXISTS `expression_exatlas_tissue_tpm`;
+CREATE TABLE `expression_exatlas_tissue_tpm` (
+  `id` varchar(60) NOT NULL,
+  `sample` varchar(60) NOT NULL,
+  `log2` double(20,14) DEFAULT NULL,
+  `gene_i` mediumint(20) unsigned DEFAULT 0 NULL,
+  `sample_i` mediumint(20) unsigned DEFAULT 0 NULL,
+  KEY `id` (`id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
+-- ----------------------------
+--  Table structure for `gene_arabidopsis`
+-- ----------------------------
+DROP TABLE IF EXISTS `gene_arabidopsis`;
+CREATE TABLE `gene_arabidopsis` (
+  `gene_id` varchar(255) NOT NULL,
+  `arabidopsis_gene_id` varchar(255) DEFAULT '' NOT NULL,
+  `gene_i` mediumint(20) unsigned DEFAULT 0 NOT NULL,
+  PRIMARY KEY (`gene_i`,`gene_id`),
+  KEY `arabidopsis_gene_id` (`arabidopsis_gene_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=COMPACT;
+
+-- ----------------------------
+--  Table structure for `gene_atg`
+-- ----------------------------
+DROP TABLE IF EXISTS `gene_atg`;
+CREATE TABLE `gene_atg` (
+  `gene_id` varchar(255) NOT NULL,
+  `atg_description` varchar(1000) DEFAULT '' NOT NULL,
+  `atg_id` varchar(255) DEFAULT '' NOT NULL,
+  `gene_i` mediumint(20) unsigned DEFAULT 0 NOT NULL,
+  PRIMARY KEY (`gene_i`,`gene_id`),
+  KEY `atg_id` (`atg_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=COMPACT;
+
+-- ----------------------------
+--  Table structure for `gene_eucalyptus`
+-- ----------------------------
+DROP TABLE IF EXISTS `gene_eucalyptus`;
+CREATE TABLE `gene_eucalyptus` (
+  `gene_id` varchar(255) NOT NULL,
+  `populus_gene_id` varchar(255) DEFAULT '' NOT NULL,
+  `gene_i` mediumint(20) unsigned DEFAULT 0 NOT NULL,
+  PRIMARY KEY (`gene_i`,`gene_id`),
+  KEY `populus_gene_id` (`populus_gene_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=COMPACT;
+
+-- ----------------------------
+--  Table structure for `gene_go`
+-- ----------------------------
+DROP TABLE IF EXISTS `gene_go`;
+CREATE TABLE `gene_go` (
+  `gene_id` varchar(255) NOT NULL,
+  `go_description` varchar(1000)  DEFAULT '' NOT NULL,
+  `go_id` varchar(255)  DEFAULT '' NOT NULL,
+  `gene_i` mediumint(20) unsigned DEFAULT 0 NOT NULL,
+  PRIMARY KEY (`gene_i`,`gene_id`),
+  KEY `go_id` (`go_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=COMPACT;
+
+-- ----------------------------
+--  Table structure for `transcript_go`
+-- ----------------------------
+DROP TABLE IF EXISTS `transcript_go`;
+CREATE TABLE `transcript_go` (
+  `transcript_id` varchar(255) NOT NULL,
+  `go_description` varchar(1000) NOT NULL DEFAULT '',
+  `go_id` varchar(255) NOT NULL DEFAULT '',
+  `transcript_i` mediumint(20) unsigned NOT NULL DEFAULT '0',
+  PRIMARY KEY (`transcript_i`,`transcript_id`),
+  KEY `go_id` (`go_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=COMPACT;
+
+-- ----------------------------
+--  Table structure for `gene_info`
+-- ----------------------------
+DROP TABLE IF EXISTS `gene_info`;
+CREATE TABLE `gene_info` (
+  `gene_id` varchar(60) NOT NULL,
+  `chromosome_name` varchar(16) NOT NULL,
+  `gene_start` int(16) unsigned NOT NULL,
+  `gene_end` int(16) unsigned NOT NULL,
+  `description` varchar(1000)  DEFAULT '' NOT NULL,
+  `gene_i` mediumint(20) unsigned NOT NULL AUTO_INCREMENT,
+  PRIMARY KEY (`gene_i`,`gene_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 AUTO_INCREMENT=1;
+
+-- ----------------------------
+--  Table structure for `gene_kegg`
+-- ----------------------------
+DROP TABLE IF EXISTS `gene_kegg`;
+CREATE TABLE `gene_kegg` (
+  `gene_id` varchar(255) NOT NULL,
+  `kegg_description` varchar(1000)  DEFAULT '' NOT NULL,
+  `kegg_id` varchar(255)  DEFAULT '' NOT NULL,
+  `gene_i` mediumint(20) unsigned DEFAULT 0 NOT NULL,
+  PRIMARY KEY (`gene_i`,`gene_id`),
+  KEY `kegg_id` (`kegg_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=COMPACT;
+
+-- ----------------------------
+--  Table structure for `gene_maize`
+-- ----------------------------
+DROP TABLE IF EXISTS `gene_maize`;
+CREATE TABLE `gene_maize` (
+  `gene_id` varchar(255) NOT NULL,
+  `maize_gene_id` varchar(255)  DEFAULT '' NOT NULL,
+  `gene_i` mediumint(20) unsigned DEFAULT 0 NOT NULL,
+  PRIMARY KEY (`gene_i`,`gene_id`),
+  KEY `maize_gene_id` (`maize_gene_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=COMPACT;
+
+-- ----------------------------
+--  Table structure for `gene_pfam`
+-- ----------------------------
+DROP TABLE IF EXISTS `gene_pfam`;
+CREATE TABLE `gene_pfam` (
+  `gene_id` varchar(255) NOT NULL,
+  `pfam_description` varchar(1000)  DEFAULT '' NOT NULL,
+  `pfam_id` varchar(255)  DEFAULT '' NOT NULL,
+  `gene_i` mediumint(20) unsigned DEFAULT 0 NOT NULL,
+  PRIMARY KEY (`gene_i`,`gene_id`),
+  KEY `pfam_id` (`pfam_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=COMPACT;
+
+-- ----------------------------
+--  Table structure for `gene_populus`
+-- ----------------------------
+DROP TABLE IF EXISTS `gene_populus`;
+CREATE TABLE `gene_populus` (
+  `gene_id` varchar(255) NOT NULL,
+  `populus_gene_id` varchar(255)  DEFAULT '' NOT NULL,
+  `gene_i` mediumint(20) unsigned DEFAULT 0 NOT NULL,
+  PRIMARY KEY (`gene_i`,`gene_id`),
+  KEY `populus_gene_id` (`populus_gene_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=COMPACT;
+
+-- ----------------------------
+--  Table structure for `gene_spruce`
+-- ----------------------------
+DROP TABLE IF EXISTS `gene_spruce`;
+CREATE TABLE `gene_spruce` (
+  `gene_id` varchar(255) NOT NULL,
+  `spruce_gene_id` varchar(255)  DEFAULT '' NOT NULL,
+  `gene_i` mediumint(20) unsigned DEFAULT 0 NOT NULL,
+  PRIMARY KEY (`gene_i`,`gene_id`),
+  KEY `spruce_gene_id` (`spruce_gene_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=COMPACT;
+
+-- ----------------------------
+--  Table structure for `sequence_color`
+-- ----------------------------
+DROP TABLE IF EXISTS `sequence_color`;
+CREATE TABLE `sequence_color` (
+  `id` varchar(255) DEFAULT NULL,
+  `scaffold` varchar(255) DEFAULT NULL,
+  `feature` varchar(255) DEFAULT NULL,
+  `start_point` varchar(255) DEFAULT NULL,
+  `end_point` varchar(255) DEFAULT NULL
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
+-- ----------------------------
+--  Table structure for `transcript_info`
+-- ----------------------------
+DROP TABLE IF EXISTS `transcript_info`;
+CREATE TABLE `transcript_info` (
+  `transcript_id` varchar(255) NOT NULL DEFAULT '',
+  `gene_id` varchar(255) NOT NULL,
+  `description` varchar(1000) DEFAULT '',
+  `chromosome_name` varchar(16) NOT NULL,
+  `strand` varchar(2) NOT NULL,
+  `gene_start` int(16) unsigned NOT NULL,
+  `gene_end` int(16) unsigned NOT NULL,
+  `pac_id` varchar(20) DEFAULT NULL,
+  `peptide_name` varchar(50) DEFAULT NULL,
+  `transcript_start` int(16) unsigned NOT NULL,
+  `transcript_end` int(16) unsigned NOT NULL,
+  `transcript_i` mediumint(20) unsigned NOT NULL AUTO_INCREMENT,
+  `gene_i` mediumint(20) unsigned DEFAULT 0 NOT NULL ,
+  PRIMARY KEY (`transcript_i`,`transcript_id`),
+  INDEX `gene_i` (`gene_i`),	
+  INDEX `gene_id` (`gene_id`)
+  INDEX `gene_id` (`transcript_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=DYNAMIC AUTO_INCREMENT=1;
+
+-- ----------------------------
+--  Table structure for `transcript_potri`
+-- ----------------------------
+DROP TABLE IF EXISTS `transcript_potri`;
+CREATE TABLE `transcript_potri` (
+  `transcript_id` varchar(255)  DEFAULT '' NOT NULL,
+  `potri_id` varchar(255)  DEFAULT '' NOT NULL,
+  `transcript_i` mediumint(20) unsigned DEFAULT 0 NOT NULL,
+  PRIMARY KEY (`transcript_i`,`transcript_id`),
+  KEY `potri_id` (`potri_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=DYNAMIC;
+
+-- ----------------------------
+--  Table structure for `transcript_atg`
+-- ----------------------------
+DROP TABLE IF EXISTS `transcript_atg`;
+CREATE TABLE `transcript_atg` (
+  `transcript_id` varchar(255) NOT NULL,
+  `atg_id` varchar(255)  DEFAULT '' NOT NULL,
+  `transcript_i` mediumint(20) unsigned DEFAULT 0 NOT NULL,
+  `description` varchar(1000)  DEFAULT '' NOT NULL,
+  PRIMARY KEY (`transcript_i`,`transcript_id`),
+  KEY `atg_id` (`atg_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=DYNAMIC;
+
+-- ----------------------------
+--  Table structure for `genebaskets`
+-- ----------------------------
+DROP TABLE IF EXISTS `genebaskets`;
+CREATE TABLE `genebaskets` (
+  `gene_basket_id` int(10) NOT NULL AUTO_INCREMENT,
+  `gene_basket_name` varchar(100) COLLATE latin1_general_ci NOT NULL,
+  `harga` bigint(16) NOT NULL,
+  `genelist` mediumtext COLLATE latin1_general_ci,
+  `ip` varchar(255) CHARACTER SET utf8 DEFAULT NULL,
+  `time` timestamp NULL DEFAULT NULL ON UPDATE CURRENT_TIMESTAMP,
+  PRIMARY KEY (`gene_basket_id`)
+) ENGINE=MyISAM AUTO_INCREMENT=1 DEFAULT CHARSET=latin1 COLLATE=latin1_general_ci;
+
+-- ----------------------------
+--  Table structure for `share_table`
+-- ----------------------------
+DROP TABLE IF EXISTS `share_table`;
+CREATE TABLE `share_table` (
+  `gene_basket_id` int(10) NOT NULL AUTO_INCREMENT,
+  `gene_basket_name` varchar(100) COLLATE latin1_general_ci NOT NULL,
+  `harga` bigint(16) NOT NULL,
+  `genelist` mediumtext COLLATE latin1_general_ci, 
+  `ip` varchar(255) COLLATE latin1_general_ci DEFAULT NULL,
+  `time` timestamp NULL DEFAULT NULL, 
+  `randid` varchar(255) COLLATE latin1_general_ci DEFAULT NULL,
+  PRIMARY KEY (`gene_basket_id`)
+) ENGINE=MyISAM AUTO_INCREMENT=1 DEFAULT CHARSET=latin1 COLLATE=latin1_general_ci;
+
+-- ---------------------------- 
+--  Table structure for `defaultgenebaskets`
+-- ----------------------------
+DROP TABLE IF EXISTS `defaultgenebaskets`;
+CREATE TABLE `defaultgenebaskets` (
+  `gene_basket_id` int(10) NOT NULL,
+  `ip` varchar(255) CHARACTER SET utf8 NOT NULL DEFAULT '',
+  `time` timestamp NULL DEFAULT NULL ON UPDATE CURRENT_TIMESTAMP,
+  PRIMARY KEY (`gene_basket_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
+SET FOREIGN_KEY_CHECKS = 1;

egrandis_demo_nodata.sql

@@ -0,0 +1,213 @@
+/*
+ Navicat Premium Data Transfer
+
+ Source Server         : Spruce
+ Source Server Type    : MySQL
+ Source Server Version : 50561
+ Source Host           : spruce.plantphys.umu.se
+ Source Database       : egrandis_demo
+
+ Target Server Type    : MySQL
+ Target Server Version : 50561
+ File Encoding         : utf-8
+
+ Date: 05/30/2019 18:02:41 PM
+*/
+
+SET NAMES utf8;
+SET FOREIGN_KEY_CHECKS = 0;
+
+-- ----------------------------
+--  Table structure for `Expression`
+-- ----------------------------
+DROP TABLE IF EXISTS `Expression`;
+CREATE TABLE `Expression` (
+  `id` varchar(255) DEFAULT NULL,
+  `sample` varchar(255) DEFAULT NULL,
+  `log2` varchar(255) DEFAULT NULL,
+  `rmd` varchar(255) DEFAULT NULL,
+  `log2fc` varchar(255) DEFAULT NULL
+) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+
+-- ----------------------------
+--  Table structure for `defaultgenebaskets`
+-- ----------------------------
+DROP TABLE IF EXISTS `defaultgenebaskets`;
+CREATE TABLE `defaultgenebaskets` (
+  `gene_basket_id` int(10) NOT NULL,
+  `ip` varchar(255) CHARACTER SET utf8 NOT NULL DEFAULT '',
+  `time` timestamp NULL DEFAULT NULL ON UPDATE CURRENT_TIMESTAMP,
+  PRIMARY KEY (`gene_basket_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
+-- ----------------------------
+--  Table structure for `expression_tissues`
+-- ----------------------------
+DROP TABLE IF EXISTS `expression_tissues`;
+CREATE TABLE `expression_tissues` (
+  `id` varchar(255) DEFAULT NULL,
+  `sample` varchar(255) DEFAULT NULL,
+  `log2` varchar(255) DEFAULT NULL,
+  `rmd` varchar(255) DEFAULT NULL,
+  `log2fc` varchar(255) DEFAULT NULL,
+  `log2dif` varchar(255) DEFAULT NULL
+) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+
+-- ----------------------------
+--  Table structure for `gene_atg`
+-- ----------------------------
+DROP TABLE IF EXISTS `gene_atg`;
+CREATE TABLE `gene_atg` (
+  `gene_id` varchar(255) NOT NULL,
+  `atg_description` varchar(255) DEFAULT NULL,
+  `atg_id` varchar(24) NOT NULL,
+  `gene_i` mediumint(11) unsigned NOT NULL,
+  PRIMARY KEY (`gene_i`,`gene_id`),
+  KEY `transcript_id` (`gene_id`),
+  KEY `atg_id` (`atg_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=COMPACT;
+
+-- ----------------------------
+--  Table structure for `gene_go`
+-- ----------------------------
+DROP TABLE IF EXISTS `gene_go`;
+CREATE TABLE `gene_go` (
+  `gene_id` varchar(255) NOT NULL,
+  `go_description` varchar(255) DEFAULT NULL,
+  `go_id` varchar(24) NOT NULL,
+  `gene_i` mediumint(11) unsigned NOT NULL,
+  PRIMARY KEY (`gene_i`,`gene_id`),
+  KEY `transcript_id` (`gene_id`),
+  KEY `atg_id` (`go_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=COMPACT;
+
+-- ----------------------------
+--  Table structure for `gene_kegg`
+-- ----------------------------
+DROP TABLE IF EXISTS `gene_kegg`;
+CREATE TABLE `gene_kegg` (
+  `gene_id` varchar(255) NOT NULL,
+  `kegg_description` varchar(255) DEFAULT NULL,
+  `kegg_id` varchar(24) NOT NULL,
+  `gene_i` mediumint(11) unsigned NOT NULL,
+  PRIMARY KEY (`gene_i`,`gene_id`),
+  KEY `transcript_id` (`gene_id`),
+  KEY `atg_id` (`kegg_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=COMPACT;
+
+-- ----------------------------
+--  Table structure for `gene_pfam`
+-- ----------------------------
+DROP TABLE IF EXISTS `gene_pfam`;
+CREATE TABLE `gene_pfam` (
+  `gene_id` varchar(255) NOT NULL,
+  `pfam_description` varchar(255) DEFAULT NULL,
+  `pfam_id` varchar(24) NOT NULL,
+  `gene_i` mediumint(11) unsigned NOT NULL,
+  PRIMARY KEY (`gene_i`,`gene_id`),
+  KEY `transcript_id` (`gene_id`),
+  KEY `atg_id` (`pfam_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=COMPACT;
+
+-- ----------------------------
+--  Table structure for `genebaskets`
+-- ----------------------------
+DROP TABLE IF EXISTS `genebaskets`;
+CREATE TABLE `genebaskets` (
+  `gene_basket_id` int(10) NOT NULL AUTO_INCREMENT,
+  `gene_basket_name` varchar(100) COLLATE latin1_general_ci NOT NULL,
+  `harga` bigint(16) NOT NULL,
+  `genelist` mediumtext COLLATE latin1_general_ci,
+  `ip` varchar(255) CHARACTER SET utf8 DEFAULT NULL,
+  `time` timestamp NULL DEFAULT NULL ON UPDATE CURRENT_TIMESTAMP,
+  PRIMARY KEY (`gene_basket_id`)
+) ENGINE=MyISAM AUTO_INCREMENT=8 DEFAULT CHARSET=latin1 COLLATE=latin1_general_ci;
+
+-- ----------------------------
+--  Table structure for `sequence_color`
+-- ----------------------------
+DROP TABLE IF EXISTS `sequence_color`;
+CREATE TABLE `sequence_color` (
+  `id` varchar(255) DEFAULT NULL,
+  `scaffold` varchar(255) DEFAULT NULL,
+  `feature` varchar(255) DEFAULT NULL,
+  `start_point` varchar(255) DEFAULT NULL,
+  `end_point` varchar(255) DEFAULT NULL
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
+-- ----------------------------
+--  Table structure for `sequence_color_copy`
+-- ----------------------------
+DROP TABLE IF EXISTS `sequence_color_copy`;
+CREATE TABLE `sequence_color_copy` (
+  `id` varchar(255) DEFAULT NULL,
+  `scaffold` varchar(255) DEFAULT NULL,
+  `feature` varchar(255) DEFAULT NULL,
+  `start_point` varchar(255) DEFAULT NULL,
+  `end_point` varchar(255) DEFAULT NULL
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
+-- ----------------------------
+--  Table structure for `share_table`
+-- ----------------------------
+DROP TABLE IF EXISTS `share_table`;
+CREATE TABLE `share_table` (
+  `gene_basket_id` int(10) NOT NULL AUTO_INCREMENT,
+  `gene_basket_name` varchar(100) COLLATE latin1_general_ci NOT NULL,
+  `harga` bigint(16) NOT NULL,
+  `genelist` mediumtext COLLATE latin1_general_ci,
+  `ip` varchar(255) COLLATE latin1_general_ci DEFAULT NULL,
+  `time` timestamp NULL DEFAULT NULL,
+  `randid` varchar(255) COLLATE latin1_general_ci DEFAULT NULL,
+  PRIMARY KEY (`gene_basket_id`)
+) ENGINE=MyISAM AUTO_INCREMENT=29 DEFAULT CHARSET=latin1 COLLATE=latin1_general_ci;
+
+-- ----------------------------
+--  Table structure for `transcript_atg`
+-- ----------------------------
+DROP TABLE IF EXISTS `transcript_atg`;
+CREATE TABLE `transcript_atg` (
+  `transcript_id` varchar(255) NOT NULL,
+  `atg_id` varchar(24) NOT NULL,
+  `transcript_i` mediumint(11) unsigned NOT NULL,
+  `description` varchar(255) DEFAULT NULL,
+  PRIMARY KEY (`transcript_i`,`transcript_id`),
+  KEY `transcript_id` (`transcript_id`),
+  KEY `atg_id` (`atg_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=COMPACT;
+
+-- ----------------------------
+--  Table structure for `transcript_info`
+-- ----------------------------
+DROP TABLE IF EXISTS `transcript_info`;
+CREATE TABLE `transcript_info` (
+  `transcript_id` varchar(255) NOT NULL DEFAULT '',
+  `gene_id` varchar(24) NOT NULL,
+  `description` varchar(255) DEFAULT '',
+  `chromosome_name` varchar(16) NOT NULL,
+  `strand` varchar(2) NOT NULL,
+  `gene_start` int(16) unsigned NOT NULL,
+  `gene_end` int(16) unsigned NOT NULL,
+  `pac_id` varchar(20) DEFAULT NULL,
+  `peptide_name` varchar(50) DEFAULT NULL,
+  `transcript_start` int(16) unsigned NOT NULL,
+  `transcript_end` int(16) unsigned NOT NULL,
+  `transcript_i` mediumint(20) unsigned NOT NULL AUTO_INCREMENT,
+  `gene_i` mediumint(20) DEFAULT NULL,
+  PRIMARY KEY (`transcript_i`,`transcript_id`)
+) ENGINE=MyISAM AUTO_INCREMENT=46281 DEFAULT CHARSET=latin1 ROW_FORMAT=DYNAMIC;
+
+-- ----------------------------
+--  Table structure for `transcript_potri`
+-- ----------------------------
+DROP TABLE IF EXISTS `transcript_potri`;
+CREATE TABLE `transcript_potri` (
+  `transcript_id` varchar(255) NOT NULL,
+  `potri_id` varchar(24) NOT NULL,
+  `transcript_i` mediumint(11) unsigned NOT NULL,
+  PRIMARY KEY (`transcript_i`,`transcript_id`),
+  KEY `transcript_id` (`transcript_id`),
+  KEY `potri_id` (`potri_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=COMPACT;
+
+SET FOREIGN_KEY_CHECKS = 1;

genie_database.sql

@@ -0,0 +1,490 @@
+/*
+ Navicat Premium Data Transfer
+
+ Source Server         : Crick_copy
+ Source Server Type    : MySQL
+ Source Server Version : 50724
+ Source Host           : 130.239.12.240
+ Source Database       : popgenie_potri_v31
+
+ Target Server Type    : MySQL
+ Target Server Version : 50724
+ File Encoding         : utf-8
+
+ Date: 01/18/2019 14:07:31 PM
+*/
+
+SET NAMES utf8;
+SET FOREIGN_KEY_CHECKS = 0;
+
+-- ----------------------------
+--  Table structure for `correlation_affy_clr`
+-- ----------------------------
+DROP TABLE IF EXISTS `correlation_affy_clr`;
+CREATE TABLE `correlation_affy_clr` (
+  `gene_i1` int(11) NOT NULL,
+  `gene_i2` int(11) NOT NULL,
+  `corr1` double(16,10) DEFAULT NULL,
+  `gene_id1` varchar(255) DEFAULT NULL,
+  `gene_id2` varchar(255) DEFAULT NULL,
+  `edg_id` int(11) unsigned NOT NULL AUTO_INCREMENT,
+  PRIMARY KEY (`edg_id`),
+  KEY `gene_i1` (`gene_i1`) USING BTREE,
+  KEY `gene_i2` (`gene_i2`) USING BTREE
+) ENGINE=MyISAM AUTO_INCREMENT=11928904 DEFAULT CHARSET=latin1;
+
+-- ----------------------------
+--  Table structure for `correlation_affy_clr_copy`
+-- ----------------------------
+DROP TABLE IF EXISTS `correlation_affy_clr_copy`;
+CREATE TABLE `correlation_affy_clr_copy` (
+  `gene_i1` int(11) DEFAULT NULL,
+  `gene_i2` int(11) DEFAULT NULL,
+  `corr1` double(16,10) DEFAULT NULL,
+  `gene_id1` varchar(255) DEFAULT NULL,
+  `gene_id2` varchar(255) DEFAULT NULL,
+  `edg_id` int(11) unsigned NOT NULL AUTO_INCREMENT,
+  PRIMARY KEY (`edg_id`)
+) ENGINE=MyISAM AUTO_INCREMENT=11928904 DEFAULT CHARSET=latin1;
+
+-- ----------------------------
+--  Table structure for `correlation_exatlas_clr`
+-- ----------------------------
+DROP TABLE IF EXISTS `correlation_exatlas_clr`;
+CREATE TABLE `correlation_exatlas_clr` (
+  `gene_i1` int(11) NOT NULL,
+  `gene_i2` int(11) NOT NULL,
+  `corr1` double(16,10) DEFAULT NULL,
+  `gene_id1` varchar(255) DEFAULT NULL,
+  `gene_id2` varchar(255) DEFAULT NULL,
+  `edg_id` int(11) unsigned NOT NULL AUTO_INCREMENT,
+  PRIMARY KEY (`edg_id`),
+  KEY `gene_i1` (`gene_i1`) USING BTREE,
+  KEY `gene_i2` (`gene_i2`) USING BTREE
+) ENGINE=MyISAM AUTO_INCREMENT=13499518 DEFAULT CHARSET=latin1;
+
+-- ----------------------------
+--  Table structure for `correlation_expatlas_clr_copy`
+-- ----------------------------
+DROP TABLE IF EXISTS `correlation_expatlas_clr_copy`;
+CREATE TABLE `correlation_expatlas_clr_copy` (
+  `gene_i1` int(11) DEFAULT NULL,
+  `gene_i2` int(11) DEFAULT NULL,
+  `corr1` double(16,10) DEFAULT NULL,
+  `gene_id1` varchar(255) DEFAULT NULL,
+  `gene_id2` varchar(255) DEFAULT NULL,
+  `edg_id` int(11) unsigned NOT NULL AUTO_INCREMENT,
+  PRIMARY KEY (`edg_id`)
+) ENGINE=MyISAM AUTO_INCREMENT=13499518 DEFAULT CHARSET=latin1;
+
+-- ----------------------------
+--  Table structure for `correlation_wood_clr`
+-- ----------------------------
+DROP TABLE IF EXISTS `correlation_wood_clr`;
+CREATE TABLE `correlation_wood_clr` (
+  `gene_i1` int(11) NOT NULL,
+  `gene_i2` int(11) NOT NULL,
+  `corr1` double(16,10) DEFAULT NULL,
+  `gene_id1` varchar(255) DEFAULT NULL,
+  `gene_id2` varchar(255) DEFAULT NULL,
+  `edg_id` int(11) unsigned NOT NULL AUTO_INCREMENT,
+  PRIMARY KEY (`edg_id`),
+  KEY `gene_i1` (`gene_i1`) USING BTREE,
+  KEY `gene_i2` (`gene_i2`) USING BTREE
+) ENGINE=MyISAM AUTO_INCREMENT=509379 DEFAULT CHARSET=latin1;
+
+-- ----------------------------
+--  Table structure for `correlation_wood_clr_copy`
+-- ----------------------------
+DROP TABLE IF EXISTS `correlation_wood_clr_copy`;
+CREATE TABLE `correlation_wood_clr_copy` (
+  `gene_i1` int(11) DEFAULT NULL,
+  `gene_i2` int(11) DEFAULT NULL,
+  `corr1` double(16,10) DEFAULT NULL,
+  `gene_id1` varchar(255) DEFAULT NULL,
+  `gene_id2` varchar(255) DEFAULT NULL,
+  `edg_id` int(11) unsigned NOT NULL AUTO_INCREMENT,
+  PRIMARY KEY (`edg_id`)
+) ENGINE=MyISAM AUTO_INCREMENT=509379 DEFAULT CHARSET=latin1;
+
+-- ----------------------------
+--  Table structure for `eplant_asp201_2014_april`
+-- ----------------------------
+DROP TABLE IF EXISTS `eplant_asp201_2014_april`;
+CREATE TABLE `eplant_asp201_2014_april` (
+  `id` varchar(255) DEFAULT '',
+  `sample` varchar(255) DEFAULT '',
+  `log2` varchar(255) DEFAULT NULL,
+  `rmd` varchar(255) DEFAULT NULL,
+  `log2fc` varchar(255) DEFAULT NULL,
+  `num` int(11) NOT NULL AUTO_INCREMENT,
+  PRIMARY KEY (`num`)
+) ENGINE=MyISAM AUTO_INCREMENT=992041 DEFAULT CHARSET=latin1 ROW_FORMAT=DYNAMIC;
+
+-- ----------------------------
+--  Table structure for `eplant_log`
+-- ----------------------------
+DROP TABLE IF EXISTS `eplant_log`;
+CREATE TABLE `eplant_log` (
+  `id` varchar(255) NOT NULL DEFAULT '',
+  `sample` varchar(255) NOT NULL DEFAULT '',
+  `log2` varchar(255) DEFAULT NULL,
+  `rmd` varchar(255) DEFAULT NULL,
+  `log2fc` varchar(255) DEFAULT NULL,
+  PRIMARY KEY (`id`,`sample`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=DYNAMIC;
+
+-- ----------------------------
+--  Table structure for `eplant_sex_new`
+-- ----------------------------
+DROP TABLE IF EXISTS `eplant_sex_new`;
+CREATE TABLE `eplant_sex_new` (
+  `id` varchar(255) NOT NULL DEFAULT '',
+  `sample` varchar(255) NOT NULL DEFAULT '',
+  `log2` varchar(255) DEFAULT NULL,
+  `rmd` varchar(255) DEFAULT NULL,
+  `log2fc` varchar(255) DEFAULT NULL,
+  `num` int(255) NOT NULL AUTO_INCREMENT,
+  PRIMARY KEY (`num`,`id`,`sample`)
+) ENGINE=MyISAM AUTO_INCREMENT=826701 DEFAULT CHARSET=latin1 ROW_FORMAT=DYNAMIC;
+
+-- ----------------------------
+--  Table structure for `experiment`
+-- ----------------------------
+DROP TABLE IF EXISTS `experiment`;
+CREATE TABLE `experiment` (
+  `experiment_id` int(11) DEFAULT NULL,
+  `experiment_name` varchar(255) DEFAULT NULL,
+  `experiment_value` varchar(255) DEFAULT NULL,
+  `experiment_table` varchar(255) DEFAULT NULL,
+  `visibility` varchar(255) DEFAULT NULL,
+  `default selection` varchar(255) DEFAULT NULL,
+  `tool_category` varchar(255) DEFAULT NULL
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
+-- ----------------------------
+--  Table structure for `expression_affy_vst`
+-- ----------------------------
+DROP TABLE IF EXISTS `expression_affy_vst`;
+CREATE TABLE `expression_affy_vst` (
+  `id` varchar(60) NOT NULL,
+  `sample` varchar(60) NOT NULL,
+  `log2` double(20,14) DEFAULT NULL,
+  `gene_i` mediumint(11) DEFAULT NULL,
+  `sample_i` mediumint(11) DEFAULT NULL,
+  `sample_name` varchar(255) DEFAULT NULL,
+  KEY `id` (`id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
+-- ----------------------------
+--  Table structure for `expression_exatlas_vst`
+-- ----------------------------
+DROP TABLE IF EXISTS `expression_exatlas_vst`;
+CREATE TABLE `expression_exatlas_vst` (
+  `id` varchar(60) NOT NULL,
+  `sample` varchar(60) NOT NULL,
+  `log2` double(20,14) DEFAULT NULL,
+  `gene_i` mediumint(11) DEFAULT NULL,
+  `sample_i` mediumint(11) DEFAULT NULL,
+  `sample_name` varchar(255) DEFAULT NULL,
+  KEY `id` (`id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
+-- ----------------------------
+--  Table structure for `expression_log_vst`
+-- ----------------------------
+DROP TABLE IF EXISTS `expression_log_vst`;
+CREATE TABLE `expression_log_vst` (
+  `id` varchar(255) NOT NULL DEFAULT '',
+  `sample` varchar(255) NOT NULL DEFAULT '',
+  `log2` varchar(255) DEFAULT NULL,
+  `sample_i` mediumint(11) DEFAULT NULL,
+  `gene_i` mediumint(11) DEFAULT NULL,
+  `sample_name` varchar(255) DEFAULT NULL,
+  PRIMARY KEY (`id`,`sample`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=DYNAMIC;
+
+-- ----------------------------
+--  Table structure for `expression_sex_vst`
+-- ----------------------------
+DROP TABLE IF EXISTS `expression_sex_vst`;
+CREATE TABLE `expression_sex_vst` (
+  `id` varchar(255) NOT NULL DEFAULT '',
+  `sample` varchar(255) NOT NULL DEFAULT '',
+  `log2` varchar(255) DEFAULT NULL,
+  `rmd` varchar(255) DEFAULT NULL,
+  `log2fc` varchar(255) DEFAULT NULL,
+  `num` int(255) NOT NULL AUTO_INCREMENT,
+  `gene_i` mediumint(11) DEFAULT NULL,
+  `sample_i` mediumint(11) DEFAULT NULL,
+  `sample_name` varchar(255) DEFAULT NULL,
+  PRIMARY KEY (`num`,`id`,`sample`)
+) ENGINE=MyISAM AUTO_INCREMENT=826701 DEFAULT CHARSET=latin1 ROW_FORMAT=DYNAMIC;
+
+-- ----------------------------
+--  Table structure for `expression_v2log_vst`
+-- ----------------------------
+DROP TABLE IF EXISTS `expression_v2log_vst`;
+CREATE TABLE `expression_v2log_vst` (
+  `id` varchar(255) NOT NULL DEFAULT '',
+  `sample` varchar(255) NOT NULL DEFAULT '',
+  `log2` varchar(255) DEFAULT NULL,
+  `rmd` varchar(255) DEFAULT NULL,
+  `log2fc` varchar(255) DEFAULT NULL,
+  `sample_i` mediumint(11) DEFAULT NULL,
+  `gene_i` mediumint(11) DEFAULT NULL,
+  PRIMARY KEY (`id`,`sample`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=DYNAMIC;
+
+-- ----------------------------
+--  Table structure for `expression_wood_vst`
+-- ----------------------------
+DROP TABLE IF EXISTS `expression_wood_vst`;
+CREATE TABLE `expression_wood_vst` (
+  `id` varchar(60) NOT NULL,
+  `sample` varchar(60) NOT NULL,
+  `log2` double(20,14) DEFAULT NULL,
+  `sample_i` mediumint(11) DEFAULT NULL,
+  `gene_i` mediumint(11) DEFAULT NULL,
+  `sample_name` varchar(255) DEFAULT NULL,
+  KEY `id` (`id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
+-- ----------------------------
+--  Table structure for `gene_arabidopsis`
+-- ----------------------------
+DROP TABLE IF EXISTS `gene_arabidopsis`;
+CREATE TABLE `gene_arabidopsis` (
+  `gene_id` varchar(255) NOT NULL,
+  `arabidopsis_gene_id` varchar(24) NOT NULL,
+  `gene_i` mediumint(11) unsigned NOT NULL,
+  PRIMARY KEY (`gene_i`,`gene_id`),
+  KEY `gene_id` (`gene_id`),
+  KEY `arabidopsis_gene_id` (`arabidopsis_gene_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=COMPACT;
+
+-- ----------------------------
+--  Table structure for `gene_atg`
+-- ----------------------------
+DROP TABLE IF EXISTS `gene_atg`;
+CREATE TABLE `gene_atg` (
+  `gene_id` varchar(255) NOT NULL,
+  `atg_description` varchar(255) DEFAULT NULL,
+  `atg_id` varchar(24) DEFAULT NULL,
+  `gene_i` mediumint(11) unsigned NOT NULL DEFAULT '0',
+  PRIMARY KEY (`gene_i`,`gene_id`),
+  KEY `gene_id` (`gene_id`),
+  KEY `atg_id` (`atg_id`),
+  KEY `gene_i` (`gene_i`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=COMPACT;
+
+-- ----------------------------
+--  Table structure for `gene_eucalyptus`
+-- ----------------------------
+DROP TABLE IF EXISTS `gene_eucalyptus`;
+CREATE TABLE `gene_eucalyptus` (
+  `gene_id` varchar(255) NOT NULL,
+  `populus_gene_id` varchar(24) NOT NULL,
+  `gene_i` mediumint(11) unsigned NOT NULL,
+  PRIMARY KEY (`gene_i`,`gene_id`),
+  KEY `gene_id` (`gene_id`),
+  KEY `populus_gene_id` (`populus_gene_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=COMPACT;
+
+-- ----------------------------
+--  Table structure for `gene_go`
+-- ----------------------------
+DROP TABLE IF EXISTS `gene_go`;
+CREATE TABLE `gene_go` (
+  `gene_id` varchar(255) NOT NULL,
+  `go_description` varchar(255) DEFAULT NULL,
+  `go_id` varchar(24) NOT NULL,
+  `gene_i` mediumint(11) unsigned NOT NULL,
+  PRIMARY KEY (`gene_i`,`gene_id`),
+  KEY `gene_id` (`gene_id`),
+  KEY `go_id` (`go_id`),
+  KEY `gene_i` (`gene_i`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=COMPACT;
+
+-- ----------------------------
+--  Table structure for `gene_info`
+-- ----------------------------
+DROP TABLE IF EXISTS `gene_info`;
+CREATE TABLE `gene_info` (
+  `gene_id` varchar(60) NOT NULL,
+  `chromosome_name` varchar(16) NOT NULL,
+  `gene_start` int(16) unsigned NOT NULL,
+  `gene_end` int(16) unsigned NOT NULL,
+  `description` varchar(255) DEFAULT '',
+  `gene_i` mediumint(20) NOT NULL AUTO_INCREMENT,
+  PRIMARY KEY (`gene_i`),
+  KEY `gene_id` (`gene_id`),
+  KEY `gene_i` (`gene_i`)
+) ENGINE=MyISAM AUTO_INCREMENT=42951 DEFAULT CHARSET=latin1;
+
+-- ----------------------------
+--  Table structure for `gene_kegg`
+-- ----------------------------
+DROP TABLE IF EXISTS `gene_kegg`;
+CREATE TABLE `gene_kegg` (
+  `gene_id` varchar(255) NOT NULL,
+  `kegg_description` varchar(255) DEFAULT NULL,
+  `kegg_id` varchar(24) NOT NULL,
+  `gene_i` mediumint(11) unsigned NOT NULL,
+  PRIMARY KEY (`gene_i`,`gene_id`),
+  KEY `gene_id` (`gene_id`),
+  KEY `kegg_id` (`kegg_id`),
+  KEY `gene_i` (`gene_i`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=COMPACT;
+
+-- ----------------------------
+--  Table structure for `gene_maize`
+-- ----------------------------
+DROP TABLE IF EXISTS `gene_maize`;
+CREATE TABLE `gene_maize` (
+  `gene_id` varchar(255) NOT NULL,
+  `maize_gene_id` varchar(24) NOT NULL,
+  `gene_i` mediumint(11) unsigned NOT NULL,
+  PRIMARY KEY (`gene_i`,`gene_id`),
+  KEY `gene_id` (`gene_id`),
+  KEY `maize_gene_id` (`maize_gene_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=COMPACT;
+
+-- ----------------------------
+--  Table structure for `gene_pfam`
+-- ----------------------------
+DROP TABLE IF EXISTS `gene_pfam`;
+CREATE TABLE `gene_pfam` (
+  `gene_id` varchar(255) NOT NULL,
+  `pfam_description` varchar(255) DEFAULT NULL,
+  `pfam_id` varchar(24) NOT NULL,
+  `gene_i` mediumint(11) unsigned NOT NULL,
+  PRIMARY KEY (`gene_i`,`gene_id`),
+  KEY `gene_id` (`gene_id`),
+  KEY `pfam_id` (`pfam_id`),
+  KEY `gene_i` (`gene_i`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=COMPACT;
+
+-- ----------------------------
+--  Table structure for `gene_populus`
+-- ----------------------------
+DROP TABLE IF EXISTS `gene_populus`;
+CREATE TABLE `gene_populus` (
+  `gene_id` varchar(255) NOT NULL,
+  `populus_gene_id` varchar(24) NOT NULL,
+  `gene_i` mediumint(11) unsigned NOT NULL,
+  PRIMARY KEY (`gene_i`,`gene_id`),
+  KEY `gene_id` (`gene_id`),
+  KEY `populus_gene_id` (`populus_gene_id`),
+  KEY `gene_i` (`gene_i`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=COMPACT;
+
+-- ----------------------------
+--  Table structure for `gene_spruce`
+-- ----------------------------
+DROP TABLE IF EXISTS `gene_spruce`;
+CREATE TABLE `gene_spruce` (
+  `gene_id` varchar(255) NOT NULL,
+  `spruce_gene_id` varchar(24) NOT NULL,
+  `gene_i` mediumint(11) unsigned NOT NULL,
+  PRIMARY KEY (`gene_i`,`gene_id`),
+  KEY `gene_id` (`gene_id`),
+  KEY `spruce_gene_id` (`spruce_gene_id`),
+  KEY `gene_i` (`gene_i`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=COMPACT;
+
+-- ----------------------------
+--  Table structure for `sample_exatlas_vst`
+-- ----------------------------
+DROP TABLE IF EXISTS `sample_exatlas_vst`;
+CREATE TABLE `sample_exatlas_vst` (
+  `sample_name` varchar(255) DEFAULT NULL,
+  `sample` varchar(255) DEFAULT NULL,
+  `sample_id` varchar(255) DEFAULT NULL,
+  `dd` varchar(255) DEFAULT NULL,
+  `ee` varchar(255) DEFAULT NULL,
+  `ff` varchar(255) DEFAULT NULL
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
+-- ----------------------------
+--  Table structure for `sequence_color`
+-- ----------------------------
+DROP TABLE IF EXISTS `sequence_color`;
+CREATE TABLE `sequence_color` (
+  `id` varchar(255) DEFAULT NULL,
+  `scaffold` varchar(255) DEFAULT NULL,
+  `feature` varchar(255) DEFAULT NULL,
+  `start_point` varchar(255) DEFAULT NULL,
+  `end_point` varchar(255) DEFAULT NULL
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
+-- ----------------------------
+--  Table structure for `synonyms2`
+-- ----------------------------
+DROP TABLE IF EXISTS `synonyms2`;
+CREATE TABLE `synonyms2` (
+  `tid` varchar(255) DEFAULT NULL,
+  `Synonyms` varchar(255) DEFAULT NULL,
+  KEY `sy` (`Synonyms`) USING BTREE
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=DYNAMIC;
+
+-- ----------------------------
+--  Table structure for `transcript_atg`
+-- ----------------------------
+DROP TABLE IF EXISTS `transcript_atg`;
+CREATE TABLE `transcript_atg` (
+  `transcript_id` varchar(255) NOT NULL,
+  `atg_id` varchar(24) NOT NULL,
+  `transcript_i` mediumint(11) unsigned NOT NULL DEFAULT '0',
+  `description` varchar(255) DEFAULT NULL,
+  PRIMARY KEY (`transcript_i`,`transcript_id`),
+  KEY `transcript_id` (`transcript_id`),
+  KEY `atg_id` (`atg_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=DYNAMIC;
+
+-- ----------------------------
+--  Table structure for `transcript_info`
+-- ----------------------------
+DROP TABLE IF EXISTS `transcript_info`;
+CREATE TABLE `transcript_info` (
+  `transcript_id` varchar(255) NOT NULL DEFAULT '',
+  `gene_id` varchar(60) NOT NULL,
+  `description` varchar(255) DEFAULT '',
+  `chromosome_name` varchar(16) NOT NULL,
+  `strand` varchar(2) NOT NULL,
+  `gene_start` int(16) unsigned NOT NULL,
+  `gene_end` int(16) unsigned NOT NULL,
+  `pac_id` varchar(20) DEFAULT NULL,
+  `peptide_name` varchar(50) DEFAULT NULL,
+  `transcript_start` int(16) unsigned NOT NULL,
+  `transcript_end` int(16) unsigned NOT NULL,
+  `transcript_i` mediumint(20) unsigned NOT NULL AUTO_INCREMENT,
+  `gene_i` mediumint(20) DEFAULT NULL,
+  PRIMARY KEY (`transcript_i`,`transcript_id`),
+  KEY `transcript_id` (`transcript_id`),
+  KEY `gene_id` (`gene_id`),
+  KEY `gene_i` (`gene_i`),
+  KEY `transcript_i` (`transcript_i`)
+) ENGINE=MyISAM AUTO_INCREMENT=63499 DEFAULT CHARSET=latin1 ROW_FORMAT=DYNAMIC;
+
+-- ----------------------------
+--  Table structure for `transcript_potri`
+-- ----------------------------
+DROP TABLE IF EXISTS `transcript_potri`;
+CREATE TABLE `transcript_potri` (
+  `transcript_id` varchar(255) NOT NULL,
+  `potri_id` varchar(255) NOT NULL,
+  `transcript_i` mediumint(11) unsigned DEFAULT NULL,
+  PRIMARY KEY (`transcript_id`),
+  KEY `transcript_id` (`transcript_id`),
+  KEY `potri_id` (`potri_id`),
+  KEY `transcript_i` (`transcript_i`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=DYNAMIC;
+
+-- ----------------------------
+--  View structure for `eplantsearch`
+-- ----------------------------
+DROP VIEW IF EXISTS `eplantsearch`;
+CREATE ALGORITHM=UNDEFINED DEFINER=`chanaka`@`%` SQL SECURITY DEFINER VIEW `eplantsearch` AS select `eplant_log`.`id` AS `id`,`eplant_log`.`sample` AS `sample`,`eplant_log`.`log2` AS `log2`,`eplant_log`.`rmd` AS `rmd`,`eplant_log`.`log2fc` AS `log2fc`,`synonyms2`.`tid` AS `tid`,`synonyms2`.`Synonyms` AS `Synonyms` from (`eplant_log` left join `synonyms2` on((`eplant_log`.`id` = `synonyms2`.`Synonyms`)));
+
+SET FOREIGN_KEY_CHECKS = 1;

genie_db.sql

@@ -0,0 +1,490 @@
+/*
+ Navicat Premium Data Transfer
+
+ Source Server         : Crick_copy
+ Source Server Type    : MySQL
+ Source Server Version : 50724
+ Source Host           : 130.239.12.240
+ Source Database       : popgenie_potri_v31
+
+ Target Server Type    : MySQL
+ Target Server Version : 50724
+ File Encoding         : utf-8
+
+ Date: 01/18/2019 14:07:31 PM
+*/
+
+SET NAMES utf8;
+SET FOREIGN_KEY_CHECKS = 0;
+
+-- ----------------------------
+--  Table structure for `correlation_affy_clr`
+-- ----------------------------
+DROP TABLE IF EXISTS `correlation_affy_clr`;
+CREATE TABLE `correlation_affy_clr` (
+  `gene_i1` int(11) NOT NULL,
+  `gene_i2` int(11) NOT NULL,
+  `corr1` double(16,10) DEFAULT NULL,
+  `gene_id1` varchar(255) DEFAULT NULL,
+  `gene_id2` varchar(255) DEFAULT NULL,
+  `edg_id` int(11) unsigned NOT NULL AUTO_INCREMENT,
+  PRIMARY KEY (`edg_id`),
+  KEY `gene_i1` (`gene_i1`) USING BTREE,
+  KEY `gene_i2` (`gene_i2`) USING BTREE
+) ENGINE=MyISAM AUTO_INCREMENT=11928904 DEFAULT CHARSET=latin1;
+
+-- ----------------------------
+--  Table structure for `correlation_affy_clr_copy`
+-- ----------------------------
+DROP TABLE IF EXISTS `correlation_affy_clr_copy`;
+CREATE TABLE `correlation_affy_clr_copy` (
+  `gene_i1` int(11) DEFAULT NULL,
+  `gene_i2` int(11) DEFAULT NULL,
+  `corr1` double(16,10) DEFAULT NULL,
+  `gene_id1` varchar(255) DEFAULT NULL,
+  `gene_id2` varchar(255) DEFAULT NULL,
+  `edg_id` int(11) unsigned NOT NULL AUTO_INCREMENT,
+  PRIMARY KEY (`edg_id`)
+) ENGINE=MyISAM AUTO_INCREMENT=11928904 DEFAULT CHARSET=latin1;
+
+-- ----------------------------
+--  Table structure for `correlation_exatlas_clr`
+-- ----------------------------
+DROP TABLE IF EXISTS `correlation_exatlas_clr`;
+CREATE TABLE `correlation_exatlas_clr` (
+  `gene_i1` int(11) NOT NULL,
+  `gene_i2` int(11) NOT NULL,
+  `corr1` double(16,10) DEFAULT NULL,
+  `gene_id1` varchar(255) DEFAULT NULL,
+  `gene_id2` varchar(255) DEFAULT NULL,
+  `edg_id` int(11) unsigned NOT NULL AUTO_INCREMENT,
+  PRIMARY KEY (`edg_id`),
+  KEY `gene_i1` (`gene_i1`) USING BTREE,
+  KEY `gene_i2` (`gene_i2`) USING BTREE
+) ENGINE=MyISAM AUTO_INCREMENT=13499518 DEFAULT CHARSET=latin1;
+
+-- ----------------------------
+--  Table structure for `correlation_expatlas_clr_copy`
+-- ----------------------------
+DROP TABLE IF EXISTS `correlation_expatlas_clr_copy`;
+CREATE TABLE `correlation_expatlas_clr_copy` (
+  `gene_i1` int(11) DEFAULT NULL,
+  `gene_i2` int(11) DEFAULT NULL,
+  `corr1` double(16,10) DEFAULT NULL,
+  `gene_id1` varchar(255) DEFAULT NULL,
+  `gene_id2` varchar(255) DEFAULT NULL,
+  `edg_id` int(11) unsigned NOT NULL AUTO_INCREMENT,
+  PRIMARY KEY (`edg_id`)
+) ENGINE=MyISAM AUTO_INCREMENT=13499518 DEFAULT CHARSET=latin1;
+
+-- ----------------------------
+--  Table structure for `correlation_wood_clr`
+-- ----------------------------
+DROP TABLE IF EXISTS `correlation_wood_clr`;
+CREATE TABLE `correlation_wood_clr` (
+  `gene_i1` int(11) NOT NULL,
+  `gene_i2` int(11) NOT NULL,
+  `corr1` double(16,10) DEFAULT NULL,
+  `gene_id1` varchar(255) DEFAULT NULL,
+  `gene_id2` varchar(255) DEFAULT NULL,
+  `edg_id` int(11) unsigned NOT NULL AUTO_INCREMENT,
+  PRIMARY KEY (`edg_id`),
+  KEY `gene_i1` (`gene_i1`) USING BTREE,
+  KEY `gene_i2` (`gene_i2`) USING BTREE
+) ENGINE=MyISAM AUTO_INCREMENT=509379 DEFAULT CHARSET=latin1;
+
+-- ----------------------------
+--  Table structure for `correlation_wood_clr_copy`
+-- ----------------------------
+DROP TABLE IF EXISTS `correlation_wood_clr_copy`;
+CREATE TABLE `correlation_wood_clr_copy` (
+  `gene_i1` int(11) DEFAULT NULL,
+  `gene_i2` int(11) DEFAULT NULL,
+  `corr1` double(16,10) DEFAULT NULL,
+  `gene_id1` varchar(255) DEFAULT NULL,
+  `gene_id2` varchar(255) DEFAULT NULL,
+  `edg_id` int(11) unsigned NOT NULL AUTO_INCREMENT,
+  PRIMARY KEY (`edg_id`)
+) ENGINE=MyISAM AUTO_INCREMENT=509379 DEFAULT CHARSET=latin1;
+
+-- ----------------------------
+--  Table structure for `eplant_asp201_2014_april`
+-- ----------------------------
+DROP TABLE IF EXISTS `eplant_asp201_2014_april`;
+CREATE TABLE `eplant_asp201_2014_april` (
+  `id` varchar(255) DEFAULT '',
+  `sample` varchar(255) DEFAULT '',
+  `log2` varchar(255) DEFAULT NULL,
+  `rmd` varchar(255) DEFAULT NULL,
+  `log2fc` varchar(255) DEFAULT NULL,
+  `num` int(11) NOT NULL AUTO_INCREMENT,
+  PRIMARY KEY (`num`)
+) ENGINE=MyISAM AUTO_INCREMENT=992041 DEFAULT CHARSET=latin1 ROW_FORMAT=DYNAMIC;
+
+-- ----------------------------
+--  Table structure for `eplant_log`
+-- ----------------------------
+DROP TABLE IF EXISTS `eplant_log`;
+CREATE TABLE `eplant_log` (
+  `id` varchar(255) NOT NULL DEFAULT '',
+  `sample` varchar(255) NOT NULL DEFAULT '',
+  `log2` varchar(255) DEFAULT NULL,
+  `rmd` varchar(255) DEFAULT NULL,
+  `log2fc` varchar(255) DEFAULT NULL,
+  PRIMARY KEY (`id`,`sample`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=DYNAMIC;
+
+-- ----------------------------
+--  Table structure for `eplant_sex_new`
+-- ----------------------------
+DROP TABLE IF EXISTS `eplant_sex_new`;
+CREATE TABLE `eplant_sex_new` (
+  `id` varchar(255) NOT NULL DEFAULT '',
+  `sample` varchar(255) NOT NULL DEFAULT '',
+  `log2` varchar(255) DEFAULT NULL,
+  `rmd` varchar(255) DEFAULT NULL,
+  `log2fc` varchar(255) DEFAULT NULL,
+  `num` int(255) NOT NULL AUTO_INCREMENT,
+  PRIMARY KEY (`num`,`id`,`sample`)
+) ENGINE=MyISAM AUTO_INCREMENT=826701 DEFAULT CHARSET=latin1 ROW_FORMAT=DYNAMIC;
+
+-- ----------------------------
+--  Table structure for `experiment`
+-- ----------------------------
+DROP TABLE IF EXISTS `experiment`;
+CREATE TABLE `experiment` (
+  `experiment_id` int(11) DEFAULT NULL,
+  `experiment_name` varchar(255) DEFAULT NULL,
+  `experiment_value` varchar(255) DEFAULT NULL,
+  `experiment_table` varchar(255) DEFAULT NULL,
+  `visibility` varchar(255) DEFAULT NULL,
+  `default selection` varchar(255) DEFAULT NULL,
+  `tool_category` varchar(255) DEFAULT NULL
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
+-- ----------------------------
+--  Table structure for `expression_affy_vst`
+-- ----------------------------
+DROP TABLE IF EXISTS `expression_affy_vst`;
+CREATE TABLE `expression_affy_vst` (
+  `id` varchar(60) NOT NULL,
+  `sample` varchar(60) NOT NULL,
+  `log2` double(20,14) DEFAULT NULL,
+  `gene_i` mediumint(11) DEFAULT NULL,
+  `sample_i` mediumint(11) DEFAULT NULL,
+  `sample_name` varchar(255) DEFAULT NULL,
+  KEY `id` (`id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
+-- ----------------------------
+--  Table structure for `expression_exatlas_vst`
+-- ----------------------------
+DROP TABLE IF EXISTS `expression_exatlas_vst`;
+CREATE TABLE `expression_exatlas_vst` (
+  `id` varchar(60) NOT NULL,
+  `sample` varchar(60) NOT NULL,
+  `log2` double(20,14) DEFAULT NULL,
+  `gene_i` mediumint(11) DEFAULT NULL,
+  `sample_i` mediumint(11) DEFAULT NULL,
+  `sample_name` varchar(255) DEFAULT NULL,
+  KEY `id` (`id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
+-- ----------------------------
+--  Table structure for `expression_log_vst`
+-- ----------------------------
+DROP TABLE IF EXISTS `expression_log_vst`;
+CREATE TABLE `expression_log_vst` (
+  `id` varchar(255) NOT NULL DEFAULT '',
+  `sample` varchar(255) NOT NULL DEFAULT '',
+  `log2` varchar(255) DEFAULT NULL,
+  `sample_i` mediumint(11) DEFAULT NULL,
+  `gene_i` mediumint(11) DEFAULT NULL,
+  `sample_name` varchar(255) DEFAULT NULL,
+  PRIMARY KEY (`id`,`sample`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=DYNAMIC;
+
+-- ----------------------------
+--  Table structure for `expression_sex_vst`
+-- ----------------------------
+DROP TABLE IF EXISTS `expression_sex_vst`;
+CREATE TABLE `expression_sex_vst` (
+  `id` varchar(255) NOT NULL DEFAULT '',
+  `sample` varchar(255) NOT NULL DEFAULT '',
+  `log2` varchar(255) DEFAULT NULL,
+  `rmd` varchar(255) DEFAULT NULL,
+  `log2fc` varchar(255) DEFAULT NULL,
+  `num` int(255) NOT NULL AUTO_INCREMENT,
+  `gene_i` mediumint(11) DEFAULT NULL,
+  `sample_i` mediumint(11) DEFAULT NULL,
+  `sample_name` varchar(255) DEFAULT NULL,
+  PRIMARY KEY (`num`,`id`,`sample`)
+) ENGINE=MyISAM AUTO_INCREMENT=826701 DEFAULT CHARSET=latin1 ROW_FORMAT=DYNAMIC;
+
+-- ----------------------------
+--  Table structure for `expression_v2log_vst`
+-- ----------------------------
+DROP TABLE IF EXISTS `expression_v2log_vst`;
+CREATE TABLE `expression_v2log_vst` (
+  `id` varchar(255) NOT NULL DEFAULT '',
+  `sample` varchar(255) NOT NULL DEFAULT '',
+  `log2` varchar(255) DEFAULT NULL,
+  `rmd` varchar(255) DEFAULT NULL,
+  `log2fc` varchar(255) DEFAULT NULL,
+  `sample_i` mediumint(11) DEFAULT NULL,
+  `gene_i` mediumint(11) DEFAULT NULL,
+  PRIMARY KEY (`id`,`sample`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=DYNAMIC;
+
+-- ----------------------------
+--  Table structure for `expression_wood_vst`
+-- ----------------------------
+DROP TABLE IF EXISTS `expression_wood_vst`;
+CREATE TABLE `expression_wood_vst` (
+  `id` varchar(60) NOT NULL,
+  `sample` varchar(60) NOT NULL,
+  `log2` double(20,14) DEFAULT NULL,
+  `sample_i` mediumint(11) DEFAULT NULL,
+  `gene_i` mediumint(11) DEFAULT NULL,
+  `sample_name` varchar(255) DEFAULT NULL,
+  KEY `id` (`id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
+-- ----------------------------
+--  Table structure for `gene_arabidopsis`
+-- ----------------------------
+DROP TABLE IF EXISTS `gene_arabidopsis`;
+CREATE TABLE `gene_arabidopsis` (
+  `gene_id` varchar(255) NOT NULL,
+  `arabidopsis_gene_id` varchar(24) NOT NULL,
+  `gene_i` mediumint(11) unsigned NOT NULL,
+  PRIMARY KEY (`gene_i`,`gene_id`),
+  KEY `gene_id` (`gene_id`),
+  KEY `arabidopsis_gene_id` (`arabidopsis_gene_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=COMPACT;
+
+-- ----------------------------
+--  Table structure for `gene_atg`
+-- ----------------------------
+DROP TABLE IF EXISTS `gene_atg`;
+CREATE TABLE `gene_atg` (
+  `gene_id` varchar(255) NOT NULL,
+  `atg_description` varchar(255) DEFAULT NULL,
+  `atg_id` varchar(24) DEFAULT NULL,
+  `gene_i` mediumint(11) unsigned NOT NULL DEFAULT '0',
+  PRIMARY KEY (`gene_i`,`gene_id`),
+  KEY `gene_id` (`gene_id`),
+  KEY `atg_id` (`atg_id`),
+  KEY `gene_i` (`gene_i`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=COMPACT;
+
+-- ----------------------------
+--  Table structure for `gene_eucalyptus`
+-- ----------------------------
+DROP TABLE IF EXISTS `gene_eucalyptus`;
+CREATE TABLE `gene_eucalyptus` (
+  `gene_id` varchar(255) NOT NULL,
+  `populus_gene_id` varchar(24) NOT NULL,
+  `gene_i` mediumint(11) unsigned NOT NULL,
+  PRIMARY KEY (`gene_i`,`gene_id`),
+  KEY `gene_id` (`gene_id`),
+  KEY `populus_gene_id` (`populus_gene_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=COMPACT;
+
+-- ----------------------------
+--  Table structure for `gene_go`
+-- ----------------------------
+DROP TABLE IF EXISTS `gene_go`;
+CREATE TABLE `gene_go` (
+  `gene_id` varchar(255) NOT NULL,
+  `go_description` varchar(255) DEFAULT NULL,
+  `go_id` varchar(24) NOT NULL,
+  `gene_i` mediumint(11) unsigned NOT NULL,
+  PRIMARY KEY (`gene_i`,`gene_id`),
+  KEY `gene_id` (`gene_id`),
+  KEY `go_id` (`go_id`),
+  KEY `gene_i` (`gene_i`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=COMPACT;
+
+-- ----------------------------
+--  Table structure for `gene_info`
+-- ----------------------------
+DROP TABLE IF EXISTS `gene_info`;
+CREATE TABLE `gene_info` (
+  `gene_id` varchar(60) NOT NULL,
+  `chromosome_name` varchar(16) NOT NULL,
+  `gene_start` int(16) unsigned NOT NULL,
+  `gene_end` int(16) unsigned NOT NULL,
+  `description` varchar(255) DEFAULT '',
+  `gene_i` mediumint(20) NOT NULL AUTO_INCREMENT,
+  PRIMARY KEY (`gene_i`),
+  KEY `gene_id` (`gene_id`),
+  KEY `gene_i` (`gene_i`)
+) ENGINE=MyISAM AUTO_INCREMENT=42951 DEFAULT CHARSET=latin1;
+
+-- ----------------------------
+--  Table structure for `gene_kegg`
+-- ----------------------------
+DROP TABLE IF EXISTS `gene_kegg`;
+CREATE TABLE `gene_kegg` (
+  `gene_id` varchar(255) NOT NULL,
+  `kegg_description` varchar(255) DEFAULT NULL,
+  `kegg_id` varchar(24) NOT NULL,
+  `gene_i` mediumint(11) unsigned NOT NULL,
+  PRIMARY KEY (`gene_i`,`gene_id`),
+  KEY `gene_id` (`gene_id`),
+  KEY `kegg_id` (`kegg_id`),
+  KEY `gene_i` (`gene_i`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=COMPACT;
+
+-- ----------------------------
+--  Table structure for `gene_maize`
+-- ----------------------------
+DROP TABLE IF EXISTS `gene_maize`;
+CREATE TABLE `gene_maize` (
+  `gene_id` varchar(255) NOT NULL,
+  `maize_gene_id` varchar(24) NOT NULL,
+  `gene_i` mediumint(11) unsigned NOT NULL,
+  PRIMARY KEY (`gene_i`,`gene_id`),
+  KEY `gene_id` (`gene_id`),
+  KEY `maize_gene_id` (`maize_gene_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=COMPACT;
+
+-- ----------------------------
+--  Table structure for `gene_pfam`
+-- ----------------------------
+DROP TABLE IF EXISTS `gene_pfam`;
+CREATE TABLE `gene_pfam` (
+  `gene_id` varchar(255) NOT NULL,
+  `pfam_description` varchar(255) DEFAULT NULL,
+  `pfam_id` varchar(24) NOT NULL,
+  `gene_i` mediumint(11) unsigned NOT NULL,
+  PRIMARY KEY (`gene_i`,`gene_id`),
+  KEY `gene_id` (`gene_id`),
+  KEY `pfam_id` (`pfam_id`),
+  KEY `gene_i` (`gene_i`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=COMPACT;
+
+-- ----------------------------
+--  Table structure for `gene_populus`
+-- ----------------------------
+DROP TABLE IF EXISTS `gene_populus`;
+CREATE TABLE `gene_populus` (
+  `gene_id` varchar(255) NOT NULL,
+  `populus_gene_id` varchar(24) NOT NULL,
+  `gene_i` mediumint(11) unsigned NOT NULL,
+  PRIMARY KEY (`gene_i`,`gene_id`),
+  KEY `gene_id` (`gene_id`),
+  KEY `populus_gene_id` (`populus_gene_id`),
+  KEY `gene_i` (`gene_i`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=COMPACT;
+
+-- ----------------------------
+--  Table structure for `gene_spruce`
+-- ----------------------------
+DROP TABLE IF EXISTS `gene_spruce`;
+CREATE TABLE `gene_spruce` (
+  `gene_id` varchar(255) NOT NULL,
+  `spruce_gene_id` varchar(24) NOT NULL,
+  `gene_i` mediumint(11) unsigned NOT NULL,
+  PRIMARY KEY (`gene_i`,`gene_id`),
+  KEY `gene_id` (`gene_id`),
+  KEY `spruce_gene_id` (`spruce_gene_id`),
+  KEY `gene_i` (`gene_i`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=COMPACT;
+
+-- ----------------------------
+--  Table structure for `sample_exatlas_vst`
+-- ----------------------------
+DROP TABLE IF EXISTS `sample_exatlas_vst`;
+CREATE TABLE `sample_exatlas_vst` (
+  `sample_name` varchar(255) DEFAULT NULL,
+  `sample` varchar(255) DEFAULT NULL,
+  `sample_id` varchar(255) DEFAULT NULL,
+  `dd` varchar(255) DEFAULT NULL,
+  `ee` varchar(255) DEFAULT NULL,
+  `ff` varchar(255) DEFAULT NULL
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
+-- ----------------------------
+--  Table structure for `sequence_color`
+-- ----------------------------
+DROP TABLE IF EXISTS `sequence_color`;
+CREATE TABLE `sequence_color` (
+  `id` varchar(255) DEFAULT NULL,
+  `scaffold` varchar(255) DEFAULT NULL,
+  `feature` varchar(255) DEFAULT NULL,
+  `start_point` varchar(255) DEFAULT NULL,
+  `end_point` varchar(255) DEFAULT NULL
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
+-- ----------------------------
+--  Table structure for `synonyms2`
+-- ----------------------------
+DROP TABLE IF EXISTS `synonyms2`;
+CREATE TABLE `synonyms2` (
+  `tid` varchar(255) DEFAULT NULL,
+  `Synonyms` varchar(255) DEFAULT NULL,
+  KEY `sy` (`Synonyms`) USING BTREE
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=DYNAMIC;
+
+-- ----------------------------
+--  Table structure for `transcript_atg`
+-- ----------------------------
+DROP TABLE IF EXISTS `transcript_atg`;
+CREATE TABLE `transcript_atg` (
+  `transcript_id` varchar(255) NOT NULL,
+  `atg_id` varchar(24) NOT NULL,
+  `transcript_i` mediumint(11) unsigned NOT NULL DEFAULT '0',
+  `description` varchar(255) DEFAULT NULL,
+  PRIMARY KEY (`transcript_i`,`transcript_id`),
+  KEY `transcript_id` (`transcript_id`),
+  KEY `atg_id` (`atg_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=DYNAMIC;
+
+-- ----------------------------
+--  Table structure for `transcript_info`
+-- ----------------------------
+DROP TABLE IF EXISTS `transcript_info`;
+CREATE TABLE `transcript_info` (
+  `transcript_id` varchar(255) NOT NULL DEFAULT '',
+  `gene_id` varchar(60) NOT NULL,
+  `description` varchar(255) DEFAULT '',
+  `chromosome_name` varchar(16) NOT NULL,
+  `strand` varchar(2) NOT NULL,
+  `gene_start` int(16) unsigned NOT NULL,
+  `gene_end` int(16) unsigned NOT NULL,
+  `pac_id` varchar(20) DEFAULT NULL,
+  `peptide_name` varchar(50) DEFAULT NULL,
+  `transcript_start` int(16) unsigned NOT NULL,
+  `transcript_end` int(16) unsigned NOT NULL,
+  `transcript_i` mediumint(20) unsigned NOT NULL AUTO_INCREMENT,
+  `gene_i` mediumint(20) DEFAULT NULL,
+  PRIMARY KEY (`transcript_i`,`transcript_id`),
+  KEY `transcript_id` (`transcript_id`),
+  KEY `gene_id` (`gene_id`),
+  KEY `gene_i` (`gene_i`),
+  KEY `transcript_i` (`transcript_i`)
+) ENGINE=MyISAM AUTO_INCREMENT=63499 DEFAULT CHARSET=latin1 ROW_FORMAT=DYNAMIC;
+
+-- ----------------------------
+--  Table structure for `transcript_potri`
+-- ----------------------------
+DROP TABLE IF EXISTS `transcript_potri`;
+CREATE TABLE `transcript_potri` (
+  `transcript_id` varchar(255) NOT NULL,
+  `potri_id` varchar(255) NOT NULL,
+  `transcript_i` mediumint(11) unsigned DEFAULT NULL,
+  PRIMARY KEY (`transcript_id`),
+  KEY `transcript_id` (`transcript_id`),
+  KEY `potri_id` (`potri_id`),
+  KEY `transcript_i` (`transcript_i`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=DYNAMIC;
+
+-- ----------------------------
+--  View structure for `eplantsearch`
+-- ----------------------------
+DROP VIEW IF EXISTS `eplantsearch`;
+CREATE ALGORITHM=UNDEFINED DEFINER=`chanaka`@`%` SQL SECURITY DEFINER VIEW `eplantsearch` AS select `eplant_log`.`id` AS `id`,`eplant_log`.`sample` AS `sample`,`eplant_log`.`log2` AS `log2`,`eplant_log`.`rmd` AS `rmd`,`eplant_log`.`log2fc` AS `log2fc`,`synonyms2`.`tid` AS `tid`,`synonyms2`.`Synonyms` AS `Synonyms` from (`eplant_log` left join `synonyms2` on((`eplant_log`.`id` = `synonyms2`.`Synonyms`)));
+
+SET FOREIGN_KEY_CHECKS = 1;

gff3_parser.py

@@ -0,0 +1,79 @@
+#!/usr/bin/env python3
+"""
+A simple parser for the GFF3 format.
+
+Test with transcripts.gff3 from
+http://www.broadinstitute.org/annotation/gebo/help/gff3.html.
+
+Format specification source:
+http://www.sequenceontology.org/gff3.shtml
+
+Version 1.1: Python3 ready
+"""
+from collections import namedtuple
+import gzip
+import urllib.request, urllib.parse, urllib.error
+
+#Initialized GeneInfo named tuple. Note: namedtuple is immutable
+gffInfoFields = ["seqid", "source", "type", "start", "end", "score", "strand", "phase", "attributes"]
+GFFRecord = namedtuple("GFFRecord", gffInfoFields)
+
+def parseGFFAttributes(attributeString):
+    """Parse the GFF3 attribute column and return a dict"""#
+    if attributeString == ".": return {}
+    ret = {}
+    for attribute in attributeString.split(";"):
+        key, value = attribute.split("=")
+        ret[urllib.parse.unquote(key)] = urllib.parse.unquote(value)
+    return ret
+
+def parseGFF3(filename):
+    """
+    A minimalistic GFF3 format parser.
+    Yields objects that contain info about a single GFF3 feature.
+    
+    Supports transparent gzip decompression.
+    """
+    #Parse with transparent decompression
+    openFunc = gzip.open if filename.endswith(".gz") else open
+    with openFunc(filename) as infile:
+        for line in infile:
+            if line.startswith("#"): continue
+            parts = line.strip().split("\t")
+            #If this fails, the file format is not standard-compatible
+            assert len(parts) == len(gffInfoFields)
+            #Normalize data
+            normalizedInfo = {
+                "seqid": None if parts[0] == "." else urllib.parse.unquote(parts[0]),
+                "source": None if parts[1] == "." else urllib.parse.unquote(parts[1]),
+                "type": None if parts[2] == "." else urllib.parse.unquote(parts[2]),
+                "start": None if parts[3] == "." else int(parts[3]),
+                "end": None if parts[4] == "." else int(parts[4]),
+                "score": None if parts[5] == "." else float(parts[5]),
+                "strand": None if parts[6] == "." else urllib.parse.unquote(parts[6]),
+                "phase": None if parts[7] == "." else urllib.parse.unquote(parts[7]),
+                "attributes": parseGFFAttributes(parts[8])
+            }
+            #Alternatively, you can emit the dictionary here, if you need mutability:
+            #    yield normalizedInfo
+            yield GFFRecord(**normalizedInfo)
+            
+
+if __name__ == "__main__":
+    import argparse
+    parser = argparse.ArgumentParser()
+    parser.add_argument("file", help="The GFF3 input file (.gz allowed)")
+    parser.add_argument("--print-records", action="store_true", help="Print all GeneInfo objects, not only")
+    parser.add_argument("--filter-type", help="Ignore records not having the given type")
+    args = parser.parse_args()
+    #Execute the parser
+    recordCount = 0
+    for record in parseGFF3(args.file):
+        #Apply filter, if any
+        if args.filter_type and record.type != args.filter_type:
+            continue
+        #Print record if specified by the user
+        if args.print_records: print(record)
+        #Access attributes like this: my_strand = record.strand
+        recordCount += 1
+    print("Total records: %d" % recordCount)

load_data.sh

@@ -0,0 +1,14 @@
+#!/bin/bash
+#load_data.sh
+#USAGE: sh load_data.sh [table_name] [filename]
+#sh load_data.sh transcript_info_x /tmp/transcript_info.tsv
+
+DB_USER='root' #'your_db_username'
+DB_PASS='root' #'your_password'
+DB='my_genie_sys_database' #'database_name'
+
+mysql  --host=localhost --user=$DB_USER --password=$DB_PASS --local_infile=1 --database=$DB <<EOFMYSQL
+TRUNCATE TABLE $1;
+ALTER TABLE $1 AUTO_INCREMENT = 1;
+load data local infile '$2' ignore INTO TABLE $1 CHARACTER SET UTF8 fields terminated by '\t' LINES TERMINATED BY '\n' ignore 0 lines;
+EOFMYSQL

network.sql

@@ -0,0 +1,5 @@
+UPDATE network_table T
+   SET T.gene_i1 = 
+     (SELECT gene_i
+     FROM gene_info A
+     WHERE concat(A.gene_id,".0") = T.gene_id1)

parse.py

@@ -0,0 +1,50 @@
+#!/usr/bin/env python
+def parse(file, store):
+        f = open(file, 'r')
+        dic = {}
+        for i in f:
+                i = i.strip("\n")
+                val = i.split("\t")
+                try:
+                        dic[val[0]] = dic[val[0]] + ";"+ val[1]+"-"+val[2]
+                except KeyError:
+                        dic[val[0]] = val[1]+"-"+val[2]
+        f.close()
+        f = open(store, 'w')
+        for i in dic.keys():
+                string = i+"\t"+dic[i]+"\t0"
+                f.write(string+"\n")
+        f.close
+
+if __name__=="__main__":
+        import sys
+        if len(sys.argv) > 1:
+                file = sys.argv[1]
+                store = sys.argv[2]
+                parse(file, store)
+        else:
+                sys.exit("No input")
+
+####INPUT
+#Eucgr.A00001	GO:0008565	protein transporter activity
+#Eucgr.A00001	GO:0031204	posttranslational protein targeting to membrane, translocation
+#Eucgr.A00004	GO:0005634	nucleus
+#Eucgr.A00006	GO:0003677	DNA binding
+#Eucgr.A00006	GO:0003824	catalytic activity
+#Eucgr.A00012	GO:0015031	protein transport
+#Eucgr.A00012	GO:0006457	protein folding
+#Eucgr.A00014	GO:0003852	2-isopropylmalate synthase activity
+#Eucgr.A00014	GO:0009098	leucine biosynthetic process
+#Eucgr.A00017	GO:0008312	7S RNA binding
+
+###OUTPUT
+#Eucgr.L00569	GO:0004672-protein kinase activity;GO:0006468-protein phosphorylation;GO:0005524-ATP binding
+#Eucgr.K00395	GO:0003723-RNA binding
+#Eucgr.A02469	GO:0004672-protein kinase activity;GO:0006468-protein phosphorylation
+#Eucgr.E01168	GO:0005089-Rho guanyl-nucleotide exchange factor activity
+#Eucgr.A02467	GO:0007275-multicellular organismal development;GO:0005634-nucleus;GO:0006511-ubiquitin-dependent protein catabolic process
+#Eucgr.E01166	GO:0016747-transferase activity, transferring acyl groups other than amino-acyl groups
+#Eucgr.A02465	GO:0006950-response to stress;GO:0051087-chaperone binding;GO:0001671-ATPase activator activity
+#Eucgr.A02464	GO:0006662-glycerol ether metabolic process;GO:0045454-cell redox homeostasis;GO:0015035-protein disulfide oxidoreductase activity
+#Eucgr.E01163	GO:0016747-transferase activity, transferring acyl groups other than amino-acyl groups
+#Eucgr.A02462	GO:0005634-nucleus;GO:0006355-regulation of transcription, DNA-templated;GO:0003677-DNA binding;GO:0003700-sequence-specific DNA binding transcription factor activity;GO:004356

sample_eucgr.sql

@@ -0,0 +1,255 @@
+SET NAMES utf8;
+SET FOREIGN_KEY_CHECKS = 0;
+
+-- ----------------------------
+--  Table structure for `correlation_expatlas_clr`
+-- ----------------------------
+DROP TABLE IF EXISTS `correlation_expatlas_clr`;
+CREATE TABLE `correlation_expatlas_clr` (
+  `edg_id` int(11) unsigned NOT NULL AUTO_INCREMENT,
+  `gene_i1` int(11) NOT NULL,
+  `gene_i2` int(11) NOT NULL,
+  `corr1` double(16,10) DEFAULT NULL,
+  PRIMARY KEY (`edg_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 AUTO_INCREMENT=1;
+
+-- ----------------------------
+--  Table structure for `expression_exatlas_tissue_tpm`
+-- ----------------------------
+DROP TABLE IF EXISTS `expression_exatlas_tissue_tpm`;
+CREATE TABLE `expression_exatlas_tissue_tpm` (
+  `id` varchar(60) NOT NULL,
+  `sample` varchar(60) NOT NULL,
+  `log2` double(20,14) DEFAULT NULL,
+  `gene_i` mediumint(20) unsigned DEFAULT 0 NULL,
+  `sample_i` mediumint(20) unsigned DEFAULT 0 NULL,
+  KEY `id` (`id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
+-- ----------------------------
+--  Table structure for `gene_arabidopsis`
+-- ----------------------------
+DROP TABLE IF EXISTS `gene_arabidopsis`;
+CREATE TABLE `gene_arabidopsis` (
+  `gene_id` varchar(255) NOT NULL,
+  `arabidopsis_gene_id` varchar(255) DEFAULT '' NOT NULL,
+  `gene_i` mediumint(20) unsigned DEFAULT 0 NOT NULL,
+  PRIMARY KEY (`gene_i`,`gene_id`),
+  KEY `arabidopsis_gene_id` (`arabidopsis_gene_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=COMPACT;
+
+-- ----------------------------
+--  Table structure for `gene_atg`
+-- ----------------------------
+DROP TABLE IF EXISTS `gene_atg`;
+CREATE TABLE `gene_atg` (
+  `gene_id` varchar(255) NOT NULL,
+  `atg_description` varchar(1000) DEFAULT '' NOT NULL,
+  `atg_id` varchar(255) DEFAULT '' NOT NULL,
+  `gene_i` mediumint(20) unsigned DEFAULT 0 NOT NULL,
+  PRIMARY KEY (`gene_i`,`gene_id`),
+  KEY `atg_id` (`atg_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=COMPACT;
+
+-- ----------------------------
+--  Table structure for `gene_eucalyptus`
+-- ----------------------------
+DROP TABLE IF EXISTS `gene_eucalyptus`;
+CREATE TABLE `gene_eucalyptus` (
+  `gene_id` varchar(255) NOT NULL,
+  `populus_gene_id` varchar(255) DEFAULT '' NOT NULL,
+  `gene_i` mediumint(20) unsigned DEFAULT 0 NOT NULL,
+  PRIMARY KEY (`gene_i`,`gene_id`),
+  KEY `populus_gene_id` (`populus_gene_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=COMPACT;
+
+-- ----------------------------
+--  Table structure for `gene_go`
+-- ----------------------------
+DROP TABLE IF EXISTS `gene_go`;
+CREATE TABLE `gene_go` (
+  `gene_id` varchar(255) NOT NULL,
+  `go_description` varchar(1000)  DEFAULT '' NOT NULL,
+  `go_id` varchar(255)  DEFAULT '' NOT NULL,
+  `gene_i` mediumint(20) unsigned DEFAULT 0 NOT NULL,
+  PRIMARY KEY (`gene_i`,`gene_id`),
+  KEY `go_id` (`go_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=COMPACT;
+
+-- ----------------------------
+--  Table structure for `gene_info`
+-- ----------------------------
+DROP TABLE IF EXISTS `gene_info`;
+CREATE TABLE `gene_info` (
+  `gene_id` varchar(60) NOT NULL,
+  `chromosome_name` varchar(16) NOT NULL,
+  `gene_start` int(16) unsigned NOT NULL,
+  `gene_end` int(16) unsigned NOT NULL,
+  `description` varchar(1000)  DEFAULT '' NOT NULL,
+  `gene_i` mediumint(20) unsigned NOT NULL AUTO_INCREMENT,
+  PRIMARY KEY (`gene_i`,`gene_id`),
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 AUTO_INCREMENT=1;
+
+-- ----------------------------
+--  Table structure for `gene_kegg`
+-- ----------------------------
+DROP TABLE IF EXISTS `gene_kegg`;
+CREATE TABLE `gene_kegg` (
+  `gene_id` varchar(255) NOT NULL,
+  `kegg_description` varchar(1000)  DEFAULT '' NOT NULL,
+  `kegg_id` varchar(255)  DEFAULT '' NOT NULL,
+  `gene_i` mediumint(20) unsigned DEFAULT 0 NOT NULL,
+  PRIMARY KEY (`gene_i`,`gene_id`),
+  KEY `kegg_id` (`kegg_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=COMPACT;
+
+-- ----------------------------
+--  Table structure for `gene_maize`
+-- ----------------------------
+DROP TABLE IF EXISTS `gene_maize`;
+CREATE TABLE `gene_maize` (
+  `gene_id` varchar(255) NOT NULL,
+  `maize_gene_id` varchar(255)  DEFAULT '' NOT NULL,
+  `gene_i` mediumint(20) unsigned DEFAULT 0 NOT NULL,
+  PRIMARY KEY (`gene_i`,`gene_id`),
+  KEY `maize_gene_id` (`maize_gene_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=COMPACT;
+
+-- ----------------------------
+--  Table structure for `gene_pfam`
+-- ----------------------------
+DROP TABLE IF EXISTS `gene_pfam`;
+CREATE TABLE `gene_pfam` (
+  `gene_id` varchar(255) NOT NULL,
+  `pfam_description` varchar(1000)  DEFAULT '' NOT NULL,
+  `pfam_id` varchar(255)  DEFAULT '' NOT NULL,
+  `gene_i` mediumint(20) unsigned DEFAULT 0 NOT NULL,
+  PRIMARY KEY (`gene_i`,`gene_id`),
+  KEY `pfam_id` (`pfam_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=COMPACT;
+
+-- ----------------------------
+--  Table structure for `gene_populus`
+-- ----------------------------
+DROP TABLE IF EXISTS `gene_populus`;
+CREATE TABLE `gene_populus` (
+  `gene_id` varchar(255) NOT NULL,
+  `populus_gene_id` varchar(255)  DEFAULT '' NOT NULL,
+  `gene_i` mediumint(20) unsigned DEFAULT 0 NOT NULL,
+  PRIMARY KEY (`gene_i`,`gene_id`),
+  KEY `populus_gene_id` (`populus_gene_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=COMPACT;
+
+-- ----------------------------
+--  Table structure for `gene_spruce`
+-- ----------------------------
+DROP TABLE IF EXISTS `gene_spruce`;
+CREATE TABLE `gene_spruce` (
+  `gene_id` varchar(255) NOT NULL,
+  `spruce_gene_id` varchar(255)  DEFAULT '' NOT NULL,
+  `gene_i` mediumint(20) unsigned DEFAULT 0 NOT NULL,
+  PRIMARY KEY (`gene_i`,`gene_id`),
+  KEY `spruce_gene_id` (`spruce_gene_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=COMPACT;
+
+-- ----------------------------
+--  Table structure for `sequence_color`
+-- ----------------------------
+DROP TABLE IF EXISTS `sequence_color`;
+CREATE TABLE `sequence_color` (
+  `id` varchar(255) DEFAULT NULL,
+  `scaffold` varchar(255) DEFAULT NULL,
+  `feature` varchar(255) DEFAULT NULL,
+  `start_point` varchar(255) DEFAULT NULL,
+  `end_point` varchar(255) DEFAULT NULL
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
+-- ----------------------------
+--  Table structure for `transcript_info`
+-- ----------------------------
+DROP TABLE IF EXISTS `transcript_info`;
+CREATE TABLE `transcript_info` (
+  `transcript_id` varchar(255) NOT NULL DEFAULT '',
+  `gene_id` varchar(255) NOT NULL,
+  `description` varchar(1000) DEFAULT '',
+  `chromosome_name` varchar(16) NOT NULL,
+  `strand` varchar(2) NOT NULL,
+  `gene_start` int(16) unsigned NOT NULL,
+  `gene_end` int(16) unsigned NOT NULL,
+  `pac_id` varchar(20) DEFAULT NULL,
+  `peptide_name` varchar(50) DEFAULT NULL,
+  `transcript_start` int(16) unsigned NOT NULL,
+  `transcript_end` int(16) unsigned NOT NULL,
+  `transcript_i` mediumint(20) unsigned NOT NULL AUTO_INCREMENT,
+  `gene_i` mediumint(20) unsigned DEFAULT 0 NOT NULL ,
+  PRIMARY KEY (`transcript_i`,`transcript_id`),
+  INDEX `gene_i` (`gene_i`),	
+  INDEX `gene_id` (`gene_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=DYNAMIC AUTO_INCREMENT=1;
+
+-- ----------------------------
+--  Table structure for `transcript_potri`
+-- ----------------------------
+DROP TABLE IF EXISTS `transcript_potri`;
+CREATE TABLE `transcript_potri` (
+  `transcript_id` varchar(255)  DEFAULT '' NOT NULL,
+  `potri_id` varchar(255)  DEFAULT '' NOT NULL,
+  `transcript_i` mediumint(20) unsigned DEFAULT 0 NOT NULL,
+  PRIMARY KEY (`transcript_i`,`transcript_id`),
+  KEY `potri_id` (`potri_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=DYNAMIC;
+
+-- ----------------------------
+--  Table structure for `transcript_atg`
+-- ----------------------------
+DROP TABLE IF EXISTS `transcript_atg`;
+CREATE TABLE `transcript_atg` (
+  `transcript_id` varchar(255) NOT NULL,
+  `atg_id` varchar(255)  DEFAULT '' NOT NULL,
+  `transcript_i` mediumint(20) unsigned DEFAULT 0 NOT NULL,
+  `description` varchar(1000)  DEFAULT '' NOT NULL,
+  PRIMARY KEY (`transcript_i`,`transcript_id`),
+  KEY `atg_id` (`atg_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=DYNAMIC;
+
+-- ----------------------------
+--  Table structure for `genebaskets`
+-- ----------------------------
+DROP TABLE IF EXISTS `genebaskets`;
+CREATE TABLE `genebaskets` (
+  `gene_basket_id` int(10) NOT NULL AUTO_INCREMENT,
+  `gene_basket_name` varchar(100) COLLATE latin1_general_ci NOT NULL,
+  `harga` bigint(16) NOT NULL,
+  `genelist` mediumtext COLLATE latin1_general_ci,
+  `ip` varchar(255) CHARACTER SET utf8 DEFAULT NULL,
+  `time` timestamp NULL DEFAULT NULL ON UPDATE CURRENT_TIMESTAMP,
+  PRIMARY KEY (`gene_basket_id`)
+) ENGINE=MyISAM AUTO_INCREMENT=1 DEFAULT CHARSET=latin1 COLLATE=latin1_general_ci;
+
+-- ----------------------------
+--  Table structure for `share_table`
+-- ----------------------------
+DROP TABLE IF EXISTS `share_table`;
+CREATE TABLE `share_table` (
+  `gene_basket_id` int(10) NOT NULL AUTO_INCREMENT,
+  `gene_basket_name` varchar(100) COLLATE latin1_general_ci NOT NULL,
+  `harga` bigint(16) NOT NULL,
+  `genelist` mediumtext COLLATE latin1_general_ci, 
+  `ip` varchar(255) COLLATE latin1_general_ci DEFAULT NULL,
+  `time` timestamp NULL DEFAULT NULL, 
+  `randid` varchar(255) COLLATE latin1_general_ci DEFAULT NULL,
+  PRIMARY KEY (`gene_basket_id`)
+) ENGINE=MyISAM AUTO_INCREMENT=1 DEFAULT CHARSET=latin1 COLLATE=latin1_general_ci;
+
+-- ---------------------------- 
+--  Table structure for `defaultgenebaskets`
+-- ----------------------------
+DROP TABLE IF EXISTS `defaultgenebaskets`;
+CREATE TABLE `defaultgenebaskets` (
+  `gene_basket_id` int(10) NOT NULL,
+  `ip` varchar(255) CHARACTER SET utf8 NOT NULL DEFAULT '',
+  `time` timestamp NULL DEFAULT NULL ON UPDATE CURRENT_TIMESTAMP,
+  PRIMARY KEY (`gene_basket_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
+SET FOREIGN_KEY_CHECKS = 1;

sequence_color.sh

@@ -0,0 +1,24 @@
+#!/bin/bash
+#sequence_color.sh
+#get the gene.gff3 file and loaded into database sequence_color table.
+#Usage: sh sequence_color.sh /mnt/spruce/www/demo/geniecms/data/Egrandis_297_v2.0.gene.gff3
+
+# if less than two arguments supplied, display  error message
+        if [  $# -le 0 ]
+        then
+                start='\033[0;33m'
+                start_0='\033[0;33m'
+                start_2='\033[0;31m'
+                end='\033[0m'
+                echo  "\nUsage:\n$0 ${start}[file_name]${end}\nEx: ${start_2}sh sequence_color.sh gene.gff3${end}
+\nWhat it does?\n${start_0}This script will read input gff3 fil[file_name] and load feature coordinates to sequence_color table.${end}\n"
+                exit 1
+        fi
+
+awk '/mRNA/{split($2,a,"=");sub(/ID=./,a[2]";");print $1;next}/gene/{;next}{sub(/ID=./,a[2]";");print $1}' FS=\; OFS=\; $1 | awk '!/#/{print $9"\t"$1"\t"$3"\t"$4"\t"$5}' > tmp &&
+sed -i 's/five_prime_UTR/5UTR/' tmp && sed -i 's/three_prime_UTR/3UTR/' tmp  &&
+/usr/bin/mysql --defaults-file="$(dirname "$0")"/.mysql.cnf --local_infile=1 <<EOFMYSQL
+TRUNCATE TABLE  sequence_color;
+LOAD DATA LOCAL INFILE "tmp" INTO TABLE sequence_color fields terminated by '\t' LINES TERMINATED BY '\n' ignore 0 lines;
+EOFMYSQL
+rm tmp

update_annotation_gene_i.sh

@@ -0,0 +1,32 @@
+#!/bin/bash
+#update_annotation_gene.sh
+
+DB_USER='root' #'your_db_username'
+DB_PASS='root' #'your_password'
+DB='my_genie_sys_database' #'database_name'
+
+# USAGE sh update_annotation_gene_i.sh gene_go
+display_usage() {
+    echo "\nUsage:\n$0 [table_name] \n"
+ }
+#UPDATE $1 INNER JOIN transcript_info on transcript_info.transcript_id = $1.transcript_id SET $1.transcript_i = transcript_info.transcript_i;
+#update transcript_info,$1 set $1.transcript_i=transcript_info.transcript_i where transcript_info.transcript_id=$1.transcript_id;
+# if less than one arguments supplied, display usage
+    if [ $# -le 0 ]
+        then
+           display_usage
+             exit 1
+    fi
+count=$(mysql --host=localhost --user=$DB_USER --password=$DB_PASS --database=$DB -sse "SHOW COLUMNS FROM $1 LIKE 'transcript_id';")
+if [ ${#count} -gt 0 ]
+then
+    mysql --host=localhost --user=$DB_USER --password=$DB_PASS --local_infile=1 --database=$DB << EOFMYSQL
+UPDATE $1 INNER JOIN transcript_info on transcript_info.transcript_id = $1.transcript_id SET $1.transcript_i = transcript_info.transcript_i;
+EOFMYSQL
+else
+    mysql --host=localhost --user=$DB_USER --password=$DB_PASS --local_infile=1 --database=$DB << EOFMYSQL
+UPDATE $1 INNER JOIN transcript_info on transcript_info.gene_id = $1.gene_id SET $1.gene_i = transcript_info.gene_i;
+EOFMYSQL
+fi
+
+

update_description.sh

@@ -0,0 +1,33 @@
+#!/bin/bash
+#update_description.sh
+
+DB_USER='root' #'your_db_username'
+DB_PASS='root' #'your_password'
+DB='my_genie_sys_database' #'database_name'
+
+# if less than two arguments supplied, display  error message
+	if [  $# -le 0 ]
+	then
+		start='\033[0;33m'
+		start_0='\033[0;33m'
+		start_2='\033[0;31m' 
+		end='\033[0m'
+		echo  "\nUsage:\n$0 ${start}[gene_info/transcript_info] [file_name]${end}\nEx: ${start_2}sh update_descriptions.sh transcript_info/gene_info potra_descriptions.tsv${end}\n\nWhat it does?\n${start_0}This script will create a two columns(ids, descriptions) temporary table and load the [file_name] into it.\nThen it will match ids column in temporary table with transcript_ids/gene_ids and update the gene/transcript descriptions.\nFinally delete the temporary table.\n${end}"
+		exit 1
+	fi
+
+table_name=$(echo $1 | awk '{split($0,a,"_");print a[1]}');
+tmp_field_name=$table_name"_id"
+mysql --host=localhost --user=$DB_USER --password=$DB_PASS --local_infile=1 --database=$DB <<EOFMYSQL
+DROP TEMPORARY TABLE  IF EXISTS tmp_tb ;
+UPDATE $1 SET description = '';
+CREATE TEMPORARY TABLE tmp_tb(gene_name VARCHAR(255),annotation VARCHAR(500), PRIMARY KEY(gene_name));
+load data local infile '$2' replace INTO TABLE tmp_tb fields terminated by '\t' LINES TERMINATED BY '\n' ignore 0 lines;
+#DROP INDEX if exists $tmp_field_name ON $tmp_field_name; 
+#ALTER TABLE $1 ADD INDEX $tmp_field_name ($tmp_field_name);
+UPDATE $1 INNER JOIN tmp_tb on tmp_tb.gene_name = $1.$tmp_field_name SET $1.description = tmp_tb.annotation;
+#select * from tmp_tb limit 100;
+DROP TEMPORARY TABLE tmp_tb;
+EOFMYSQL
+#Following line is very important when we load data into the corresponding table. If we did not make index it takes so long time to load.
+#ALTER TABLE transcript_info ADD INDEX `transcript_id` (`transcript_id`)

update_gene_i.sh

@@ -0,0 +1,16 @@
+#!/bin/bash
+#update_gene_i.sh
+
+#USAGE: sh update_gene_i.sh
+DB_USER='root' #'your_db_username'
+DB_PASS='root' #'your_password'
+DB='my_genie_sys_database' #'database_name'
+
+mysql --host=localhost --user=$DB_USER --password=$DB_PASS --local_infile=1 --database=$DB   <<EOFMYSQL
+create temporary table add_gene_i(gene_i MEDIUMINT NOT NULL AUTO_INCREMENT PRIMARY KEY, genename VARCHAR(40));
+ALTER TABLE add_gene_i AUTO_INCREMENT = 1;
+INSERT INTO add_gene_i(genename) select DISTINCT(gene_id) from transcript_info;
+UPDATE transcript_info INNER join add_gene_i ON add_gene_i.genename = transcript_info.gene_id SET transcript_info.gene_i = add_gene_i.gene_i;
+drop temporary table add_gene_i;
+EOFMYSQL
+

update_gene_i_dev.sh

@@ -0,0 +1,13 @@
+#update_gene_i_dev.sh script
+#!/bin/bash
+#update_gene_i_dev.sh
+
+DB_USER='root' #'your_db_username'
+DB_PASS='root' #'your_password'
+DB='my_genie_sys_database' #'database_name'
+
+#USAGE: sh update_gene_i_dev.sh
+
+mysql --host=localhost --user=$DB_USER --password=$DB_PASS --local_infile=1 --database=$DB <<EOFMYSQL
+update transcript_info,gene_info set transcript_info.gene_i=gene_info.gene_i where gene_info.gene_id=transcript_info.gene_id;
+EOFMYSQL

update_transcript_i.sh

@@ -0,0 +1,19 @@
+#!/bin/bash
+#update_transcripts,sh
+
+#USAGE sh update.sh transcript_potri
+
+display_usage() {
+        echo  "\nUsage:\n$0 [table_name] \n"
+}
+
+# if less than one arguments supplied, display usage
+        if [  $# -le 0 ]
+        then
+                display_usage
+                exit 1
+        fi
+
+/usr/bin/mysql --defaults-file="$(dirname "$0")"/.mysql.cnf --local_infile=1 <<EOFMYSQL
+UPDATE $1 INNER JOIN transcript_info on transcript_info.transcript_id = $1.transcript_id SET $1.transcript_i = transcript_info.transcript_i;
+EOFMYSQL

zmarina.sql

@@ -0,0 +1,189 @@
+/*
+ Source Server Type    : MySQL
+ Source Server Version : 50558
+
+ Source Database       : zmarina
+
+ Target Server Type    : MySQL
+ Target Server Version : 50558
+ File Encoding         : utf-8
+
+ Date: 12/04/2017 18:55:49 PM
+*/
+
+SET NAMES utf8;
+SET FOREIGN_KEY_CHECKS = 0;
+
+-- ----------------------------
+--  Table structure for `defaultgenebaskets`
+-- ----------------------------
+DROP TABLE IF EXISTS `defaultgenebaskets`;
+CREATE TABLE `defaultgenebaskets` (
+  `gene_basket_id` int(10) NOT NULL,
+  `ip` varchar(255) CHARACTER SET utf8 NOT NULL DEFAULT '',
+  `time` timestamp NULL DEFAULT NULL ON UPDATE CURRENT_TIMESTAMP
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
+-- ----------------------------
+--  Table structure for `gene_atg`
+-- ----------------------------
+DROP TABLE IF EXISTS `gene_atg`;
+CREATE TABLE `gene_atg` (
+  `gene_id` varchar(255) NOT NULL,
+  `atg_description` varchar(255) DEFAULT NULL,
+  `atg_id` varchar(24) NOT NULL,
+  `gene_i` mediumint(11) unsigned NOT NULL,
+  PRIMARY KEY (`gene_i`,`gene_id`),
+  KEY `transcript_id` (`gene_id`),
+  KEY `atg_id` (`atg_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=COMPACT;
+
+-- ----------------------------
+--  Table structure for `gene_go`
+-- ----------------------------
+DROP TABLE IF EXISTS `gene_go`;
+CREATE TABLE `gene_go` (
+  `gene_id` varchar(255) NOT NULL,
+  `go_description` varchar(255) DEFAULT NULL,
+  `go_id` varchar(24) NOT NULL,
+  `gene_i` mediumint(11) unsigned NOT NULL,
+  PRIMARY KEY (`gene_i`,`gene_id`),
+  KEY `atg_id` (`go_id`),
+  KEY `transcript_id` (`gene_i`) USING BTREE
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=COMPACT;
+
+-- ----------------------------
+--  Table structure for `gene_info`
+-- ----------------------------
+DROP TABLE IF EXISTS `gene_info`;
+CREATE TABLE `gene_info` (
+  `gene_id` varchar(60) NOT NULL,
+  `chromosome_name` varchar(16) NOT NULL,
+  `gene_start` int(16) unsigned NOT NULL,
+  `gene_end` int(16) unsigned NOT NULL,
+  `description` varchar(255) DEFAULT '',
+  `gene_i` mediumint(20) NOT NULL AUTO_INCREMENT,
+ PRIMARY KEY (`gene_id`,`gene_i`),
+  KEY `gene_id` (`gene_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
+-- ----------------------------
+--  Table structure for `gene_kegg`
+-- ----------------------------
+DROP TABLE IF EXISTS `gene_kegg`;
+CREATE TABLE `gene_kegg` (
+  `gene_id` varchar(255) NOT NULL,
+  `kegg_description` varchar(255) DEFAULT NULL,
+  `kegg_id` varchar(24) NOT NULL,
+  `gene_i` mediumint(11) unsigned NOT NULL,
+  PRIMARY KEY (`gene_i`,`gene_id`),
+  KEY `transcript_id` (`gene_id`),
+  KEY `atg_id` (`kegg_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=COMPACT;
+
+-- ----------------------------
+--  Table structure for `gene_pfam`
+-- ----------------------------
+DROP TABLE IF EXISTS `gene_pfam`;
+CREATE TABLE `gene_pfam` (
+  `gene_id` varchar(255) NOT NULL,
+  `pfam_description` varchar(255) DEFAULT NULL,
+  `pfam_id` varchar(24) NOT NULL,
+  `gene_i` mediumint(11) unsigned NOT NULL,
+  PRIMARY KEY (`gene_id`,`gene_i`),
+  KEY `atg_id` (`pfam_id`),
+  KEY `transcript_id` (`gene_i`) USING BTREE
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=COMPACT;
+
+-- ----------------------------
+--  Table structure for `genebaskets`
+-- ----------------------------
+DROP TABLE IF EXISTS `genebaskets`;
+CREATE TABLE `genebaskets` (
+  `gene_basket_id` int(10) NOT NULL AUTO_INCREMENT,
+  `gene_basket_name` varchar(100) COLLATE latin1_general_ci NOT NULL,
+  `harga` bigint(16) NOT NULL,
+  `genelist` mediumtext COLLATE latin1_general_ci,
+  `ip` varchar(255) CHARACTER SET utf8 DEFAULT NULL,
+  `time` timestamp NULL DEFAULT NULL ON UPDATE CURRENT_TIMESTAMP,
+  PRIMARY KEY (`gene_basket_id`)
+) ENGINE=MyISAM AUTO_INCREMENT=8 DEFAULT CHARSET=latin1 COLLATE=latin1_general_ci;
+
+-- ----------------------------
+--  Table structure for `sequence_color`
+-- ----------------------------
+DROP TABLE IF EXISTS `sequence_color`;
+CREATE TABLE `sequence_color` (
+  `id` varchar(255) DEFAULT NULL,
+  `scaffold` varchar(255) DEFAULT NULL,
+  `feature` varchar(255) DEFAULT NULL,
+  `start_point` varchar(255) DEFAULT NULL,
+  `end_point` varchar(255) DEFAULT NULL
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
+-- ----------------------------
+--  Table structure for `share_table`
+-- ----------------------------
+DROP TABLE IF EXISTS `share_table`;
+CREATE TABLE `share_table` (
+  `gene_basket_id` int(10) NOT NULL AUTO_INCREMENT,
+  `gene_basket_name` varchar(100) COLLATE latin1_general_ci NOT NULL,
+  `harga` bigint(16) NOT NULL,
+  `genelist` mediumtext COLLATE latin1_general_ci,
+  `ip` varchar(255) COLLATE latin1_general_ci DEFAULT NULL,
+  `time` timestamp NULL DEFAULT NULL,
+  `randid` varchar(255) COLLATE latin1_general_ci DEFAULT NULL,
+  PRIMARY KEY (`gene_basket_id`)
+) ENGINE=MyISAM AUTO_INCREMENT=3 DEFAULT CHARSET=latin1 COLLATE=latin1_general_ci;
+
+-- ----------------------------
+--  Table structure for `transcript_atg`
+-- ----------------------------
+DROP TABLE IF EXISTS `transcript_atg`;
+CREATE TABLE `transcript_atg` (
+  `transcript_id` varchar(255) NOT NULL,
+  `atg_id` varchar(24) NOT NULL,
+  `transcript_i` mediumint(11) unsigned NOT NULL,
+  `description` varchar(255) DEFAULT NULL,
+  PRIMARY KEY (`transcript_i`,`transcript_id`),
+  KEY `transcript_id` (`transcript_id`),
+  KEY `atg_id` (`atg_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=COMPACT;
+
+-- ----------------------------
+--  Table structure for `transcript_info`
+-- ----------------------------
+DROP TABLE IF EXISTS `transcript_info`;
+CREATE TABLE `transcript_info` (
+  `transcript_id` varchar(255) NOT NULL DEFAULT '',
+  `gene_id` varchar(60) NOT NULL,
+  `description` varchar(255) DEFAULT '',
+  `chromosome_name` varchar(16) NOT NULL,
+  `strand` varchar(2) NOT NULL,
+  `gene_start` int(16) unsigned NOT NULL,
+  `gene_end` int(16) unsigned NOT NULL,
+  `pac_id` varchar(20) DEFAULT NULL,
+  `peptide_name` varchar(50) DEFAULT NULL,
+  `transcript_start` int(16) unsigned NOT NULL,
+  `transcript_end` int(16) unsigned NOT NULL,
+  `transcript_i` mediumint(20) unsigned NOT NULL AUTO_INCREMENT,
+  `gene_i` mediumint(20) DEFAULT NULL,
+  PRIMARY KEY (`transcript_i`,`transcript_id`),
+  KEY `transcript_id` (`transcript_id`),
+  KEY `transcript_i` (`transcript_i`)
+) ENGINE=MyISAM AUTO_INCREMENT=20451 DEFAULT CHARSET=latin1 ROW_FORMAT=DYNAMIC;
+
+-- ----------------------------
+--  Table structure for `transcript_potri`
+-- ----------------------------
+DROP TABLE IF EXISTS `transcript_potri`;
+CREATE TABLE `transcript_potri` (
+  `transcript_id` varchar(255) NOT NULL,
+  `potri_id` varchar(24) NOT NULL,
+  `transcript_i` mediumint(11) unsigned NOT NULL,
+  PRIMARY KEY (`transcript_i`,`transcript_id`),
+  KEY `transcript_id` (`transcript_id`),
+  KEY `potri_id` (`potri_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 ROW_FORMAT=COMPACT;
+
+SET FOREIGN_KEY_CHECKS = 1;