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schema.sql
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schema.sql
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drop table if exists medip_roi;
create table medip_roi (
id int primary key auto_increment not null,
roi_name varchar(40) not null,
unique key (roi_name)
);
drop table if exists medip_probe;
create table medip_probe (
id int primary key auto_increment not null,
roi int not null,
probe_name varchar(40) not null,
chr varchar(40) not null,
min_pos int not null,
max_pos int not null,
unique key (probe_name),
key roi_idx (roi),
key probe_genomic_idx (chr, min_pos, max_pos)
);
drop table if exists medip_expt;
create table medip_expt (
id int primary key auto_increment not null,
expt_name varchar(40) not null,
array_id varchar(40) not null,
tissue varchar(40) not null,
sample varchar(40) not null,
cy3 enum('IP', 'INPUT', 'UNKNOWN'),
cy5 enum('IP', 'INPUT', 'UNKNOWN')
);
drop table if exists medip_data;
create table medip_data (
probe int not null,
expt int not null,
log_ratio double,
unique key data_idx (probe, expt)
);
drop table if exists xmeth_coupling_profile;
create table xmeth_coupling_profile (
profile_name varchar(40) not null,
offset int not null,
coupling double not null,
unique key pos_idx (profile_name, offset)
);
drop table if exists xmeth_array_meta;
create table xmeth_array_meta (
expt int not null,
response double not null,
baseline double not null,
unique key expt_idx (expt)
);
drop table if exists xmeth_genome_sequence;
create table xmeth_genome_sequence (
assembly varchar(40) not null,
seq_name varchar(40) not null,
dna longtext not null,
unique key seq_idx (assembly, seq_name)
);
drop table if exists xmeth_genome_fragment;
create table xmeth_genome_fragment (
assembly varchar(40) not null,
seq_name varchar(40) not null,
seq_min int not null,
seq_max int not null,
dna longtext,
unique key seq_frag_idx (seq_name, seq_min, seq_max)
);
drop table if exists xmeth_array_grouping;
create table xmeth_array_grouping (
expt int not null,
expt_group varchar(40) not null,
key group_idx (expt_group)
);
drop table if exists xmeth_window_quantitation;
create table xmeth_window_quantitation (
seq_name varchar(40) not null,
seq_min int not null,
seq_max int not null,
tissue varchar(40) not null,
meth_mean double not null,
meth_var double not null,
key wq_seq_idx (seq_name, seq_min, seq_max)
);
drop table if exists xmeth_window_beta;
create table xmeth_window_beta (
seq_name varchar(40) not null,
seq_min int not null,
seq_max int not null,
tissue varchar(40) not null,
meth_alpha double not null,
meth_beta double not null,
key wb_seq_idx (seq_name, seq_min, seq_max)
);