patch mouse test data

modules/t/test-genome-DBs/mus_musculus/core/meta.txt

 1	\N	schema_type	core
-2	\N	schema_version	82
+2	\N	schema_version	83
 3	\N	patch	patch_65_66_a.sql|schema_version
 4	\N	patch	patch_65_66_b.sql|fix_external_db_id
 5	\N	patch	patch_65_66_c.sql|reorder_unmapped_obj_index
@@ -146,3 +146,4 @@
 1653	1	species.classification	Opisthokonta
 1654	1	species.classification	Eukaryota
 1660	1	species.division	Ensembl
+1661	\N	patch	patch_82_83_a.sql|schema_version

modules/t/test-genome-DBs/mus_musculus/variation/SQLite/table.sql

+-- 
+-- Created by SQL::Translator::Producer::SQLite
+-- Created on Thu Nov 12 12:46:48 2015
+-- 
+
+BEGIN TRANSACTION;
+
+--
+-- Table: allele
+--
+CREATE TABLE allele (
+  allele_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  variation_id integer NOT NULL,
+  subsnp_id integer,
+  allele_code_id integer NOT NULL,
+  population_id integer,
+  frequency float,
+  count integer,
+  frequency_submitter_handle integer
+);
+
+--
+-- Table: allele_code
+--
+CREATE TABLE allele_code (
+  allele_code_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  allele varchar(100)
+);
+
+CREATE UNIQUE INDEX allele_idx ON allele_code (allele);
+
+--
+-- Table: associate_study
+--
+CREATE TABLE associate_study (
+  study1_id integer NOT NULL,
+  study2_id integer NOT NULL,
+  PRIMARY KEY (study1_id, study2_id)
+);
+
+--
+-- Table: attrib
+--
+CREATE TABLE attrib (
+  attrib_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL DEFAULT 0,
+  attrib_type_id smallint NOT NULL DEFAULT 0,
+  value text NOT NULL
+);
+
+CREATE UNIQUE INDEX type_val_idx ON attrib (attrib_type_id, value);
+
+--
+-- Table: attrib_set
+--
+CREATE TABLE attrib_set (
+  attrib_set_id integer NOT NULL DEFAULT 0,
+  attrib_id integer NOT NULL DEFAULT 0
+);
+
+CREATE UNIQUE INDEX set_idx ON attrib_set (attrib_set_id, attrib_id);
+
+--
+-- Table: attrib_type
+--
+CREATE TABLE attrib_type (
+  attrib_type_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL DEFAULT 0,
+  code varchar(20) NOT NULL DEFAULT '',
+  name varchar(255) NOT NULL DEFAULT '',
+  description text
+);
+
+CREATE UNIQUE INDEX code_idx ON attrib_type (code);
+
+--
+-- Table: compressed_genotype_region
+--
+CREATE TABLE compressed_genotype_region (
+  sample_id integer NOT NULL,
+  seq_region_id integer NOT NULL,
+  seq_region_start integer NOT NULL,
+  seq_region_end integer NOT NULL,
+  seq_region_strand tinyint NOT NULL,
+  genotypes blob
+);
+
+--
+-- Table: compressed_genotype_var
+--
+CREATE TABLE compressed_genotype_var (
+  variation_id integer NOT NULL,
+  subsnp_id integer,
+  genotypes blob
+);
+
+--
+-- Table: coord_system
+--
+CREATE TABLE coord_system (
+  coord_system_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  species_id integer NOT NULL DEFAULT 1,
+  name varchar(40) NOT NULL,
+  version varchar(255),
+  rank integer NOT NULL,
+  attrib varchar
+);
+
+CREATE UNIQUE INDEX name_idx ON coord_system (name, version, species_id);
+
+CREATE UNIQUE INDEX rank_idx ON coord_system (rank, species_id);
+
+--
+-- Table: display_group
+--
+CREATE TABLE display_group (
+  display_group_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  display_priority integer NOT NULL,
+  display_name varchar(255) NOT NULL
+);
+
+CREATE UNIQUE INDEX display_name ON display_group (display_name);
+
+CREATE UNIQUE INDEX display_priority ON display_group (display_priority);
+
+--
+-- Table: failed_allele
+--
+CREATE TABLE failed_allele (
+  failed_allele_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  allele_id integer NOT NULL,
+  failed_description_id integer NOT NULL
+);
+
+CREATE UNIQUE INDEX allele_idx02 ON failed_allele (allele_id, failed_description_id);
+
+--
+-- Table: failed_description
+--
+CREATE TABLE failed_description (
+  failed_description_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  description text NOT NULL
+);
+
+--
+-- Table: failed_structural_variation
+--
+CREATE TABLE failed_structural_variation (
+  failed_structural_variation_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  structural_variation_id integer NOT NULL,
+  failed_description_id integer NOT NULL
+);
+
+CREATE UNIQUE INDEX structural_variation_idx ON failed_structural_variation (structural_variation_id, failed_description_id);
+
+--
+-- Table: failed_variation
+--
+CREATE TABLE failed_variation (
+  failed_variation_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  variation_id integer NOT NULL,
+  failed_description_id integer NOT NULL
+);
+
+CREATE UNIQUE INDEX variation_idx ON failed_variation (variation_id, failed_description_id);
+
+--
+-- Table: genotype_code
+--
+CREATE TABLE genotype_code (
+  genotype_code_id integer NOT NULL,
+  allele_code_id integer NOT NULL,
+  haplotype_id tinyint NOT NULL,
+  phased tinyint
+);
+
+--
+-- Table: individual
+--
+CREATE TABLE individual (
+  individual_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  name varchar(255),
+  description text,
+  gender enum NOT NULL DEFAULT 'Unknown',
+  father_individual_id integer,
+  mother_individual_id integer,
+  individual_type_id integer NOT NULL DEFAULT 0
+);
+
+--
+-- Table: individual_synonym
+--
+CREATE TABLE individual_synonym (
+  synonym_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  individual_id integer NOT NULL,
+  source_id integer NOT NULL,
+  name varchar(255)
+);
+
+--
+-- Table: individual_type
+--
+CREATE TABLE individual_type (
+  individual_type_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  name varchar(255) NOT NULL,
+  description text
+);
+
+--
+-- Table: meta
+--
+CREATE TABLE meta (
+  meta_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  species_id integer DEFAULT 1,
+  meta_key varchar(40) NOT NULL,
+  meta_value varchar(255) NOT NULL
+);
+
+CREATE UNIQUE INDEX species_key_value_idx ON meta (species_id, meta_key, meta_value);
+
+--
+-- Table: meta_coord
+--
+CREATE TABLE meta_coord (
+  table_name varchar(40) NOT NULL,
+  coord_system_id integer NOT NULL,
+  max_length integer
+);
+
+CREATE UNIQUE INDEX table_name ON meta_coord (table_name, coord_system_id);
+
+--
+-- Table: motif_feature_variation
+--
+CREATE TABLE motif_feature_variation (
+  motif_feature_variation_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  variation_feature_id integer NOT NULL,
+  feature_stable_id varchar(128),
+  motif_feature_id integer NOT NULL,
+  allele_string text,
+  somatic tinyint NOT NULL DEFAULT 0,
+  consequence_types varchar,
+  motif_name varchar(60),
+  motif_start integer,
+  motif_end integer,
+  motif_score_delta float,
+  in_informative_position tinyint NOT NULL DEFAULT 0
+);
+
+--
+-- Table: phenotype
+--
+CREATE TABLE phenotype (
+  phenotype_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  stable_id varchar(255),
+  name varchar(50),
+  description varchar(255)
+);
+
+CREATE UNIQUE INDEX desc_idx ON phenotype (description);
+
+--
+-- Table: phenotype_feature
+--
+CREATE TABLE phenotype_feature (
+  phenotype_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  phenotype_id integer,
+  source_id integer,
+  study_id integer,
+  type enum,
+  object_id varchar(255),
+  is_significant tinyint DEFAULT 1,
+  seq_region_id integer,
+  seq_region_start integer,
+  seq_region_end integer,
+  seq_region_strand tinyint
+);
+
+--
+-- Table: phenotype_feature_attrib
+--
+CREATE TABLE phenotype_feature_attrib (
+  phenotype_feature_id integer NOT NULL,
+  attrib_type_id integer,
+  value varchar(255)
+);
+
+--
+-- Table: population
+--
+CREATE TABLE population (
+  population_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  name varchar(255),
+  size integer,
+  description text,
+  collection tinyint DEFAULT 0,
+  freqs_from_gts tinyint,
+  display enum DEFAULT 'UNDISPLAYABLE',
+  display_group_id tinyint
+);
+
+--
+-- Table: population_genotype
+--
+CREATE TABLE population_genotype (
+  population_genotype_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  variation_id integer NOT NULL,
+  subsnp_id integer,
+  genotype_code_id integer,
+  frequency float,
+  population_id integer,
+  count integer
+);
+
+--
+-- Table: population_structure
+--
+CREATE TABLE population_structure (
+  super_population_id integer NOT NULL,
+  sub_population_id integer NOT NULL
+);
+
+CREATE UNIQUE INDEX super_population_idx ON population_structure (super_population_id, sub_population_id);
+
+--
+-- Table: population_synonym
+--
+CREATE TABLE population_synonym (
+  synonym_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  population_id integer NOT NULL,
+  source_id integer NOT NULL,
+  name varchar(255)
+);
+
+--
+-- Table: protein_function_predictions
+--
+CREATE TABLE protein_function_predictions (
+  translation_md5_id integer NOT NULL,
+  analysis_attrib_id integer NOT NULL,
+  prediction_matrix mediumblob,
+  PRIMARY KEY (translation_md5_id, analysis_attrib_id)
+);
+
+--
+-- Table: protein_function_predictions_attrib
+--
+CREATE TABLE protein_function_predictions_attrib (
+  translation_md5_id integer NOT NULL,
+  analysis_attrib_id integer NOT NULL,
+  attrib_type_id integer NOT NULL,
+  position_values blob,
+  PRIMARY KEY (translation_md5_id, analysis_attrib_id, attrib_type_id)
+);
+
+--
+-- Table: publication
+--
+CREATE TABLE publication (
+  publication_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  title varchar(255),
+  authors varchar(255),
+  pmid integer,
+  pmcid varchar(255),
+  year integer,
+  doi varchar(50),
+  ucsc_id varchar(50)
+);
+
+--
+-- Table: read_coverage
+--
+CREATE TABLE read_coverage (
+  seq_region_id integer NOT NULL,
+  seq_region_start integer NOT NULL,
+  seq_region_end integer NOT NULL,
+  level tinyint NOT NULL,
+  sample_id integer NOT NULL
+);
+
+--
+-- Table: regulatory_feature_variation
+--
+CREATE TABLE regulatory_feature_variation (
+  regulatory_feature_variation_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  variation_feature_id integer NOT NULL,
+  feature_stable_id varchar(128),
+  feature_type text,
+  allele_string text,
+  somatic tinyint NOT NULL DEFAULT 0,
+  consequence_types varchar
+);
+
+--
+-- Table: sample
+--
+CREATE TABLE sample (
+  sample_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  individual_id integer NOT NULL,
+  name varchar(255),
+  description text,
+  study_id integer,
+  display enum DEFAULT 'UNDISPLAYABLE',
+  has_coverage tinyint NOT NULL DEFAULT 0,
+  variation_set_id varchar
+);
+
+--
+-- Table: sample_genotype_multiple_bp
+--
+CREATE TABLE sample_genotype_multiple_bp (
+  variation_id integer NOT NULL,
+  subsnp_id integer,
+  allele_1 varchar(100),
+  allele_2 varchar(100),
+  sample_id integer
+);
+
+--
+-- Table: sample_population
+--
+CREATE TABLE sample_population (
+  sample_id integer NOT NULL,
+  population_id integer NOT NULL
+);
+
+--
+-- Table: seq_region
+--
+CREATE TABLE seq_region (
+  seq_region_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  name varchar(40) NOT NULL,
+  coord_system_id integer NOT NULL
+);
+
+CREATE UNIQUE INDEX name_cs_idx ON seq_region (name, coord_system_id);
+
+--
+-- Table: source
+--
+CREATE TABLE source (
+  source_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  name varchar(24) NOT NULL,
+  version integer,
+  description varchar(255),
+  url varchar(255),
+  type enum,
+  somatic_status enum DEFAULT 'germline',
+  data_types varchar
+);
+
+--
+-- Table: structural_variation
+--
+CREATE TABLE structural_variation (
+  structural_variation_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  variation_name varchar(255),
+  alias varchar(255),
+  source_id integer NOT NULL,
+  study_id integer,
+  class_attrib_id integer NOT NULL DEFAULT 0,
+  clinical_significance varchar,
+  validation_status enum,
+  is_evidence tinyint DEFAULT 0,
+  somatic tinyint NOT NULL DEFAULT 0,
+  copy_number tinyint
+);
+
+CREATE UNIQUE INDEX variation_name ON structural_variation (variation_name);
+
+--
+-- Table: structural_variation_association
+--
+CREATE TABLE structural_variation_association (
+  structural_variation_id integer NOT NULL,
+  supporting_structural_variation_id integer NOT NULL,
+  PRIMARY KEY (structural_variation_id, supporting_structural_variation_id)
+);
+
+--
+-- Table: structural_variation_feature
+--
+CREATE TABLE structural_variation_feature (
+  structural_variation_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  seq_region_id integer NOT NULL,
+  outer_start integer,
+  seq_region_start integer NOT NULL,
+  inner_start integer,
+  inner_end integer,
+  seq_region_end integer NOT NULL,
+  outer_end integer,
+  seq_region_strand tinyint NOT NULL,
+  structural_variation_id integer NOT NULL,
+  variation_name varchar(255),
+  source_id integer NOT NULL,
+  study_id integer,
+  class_attrib_id integer NOT NULL DEFAULT 0,
+  allele_string longtext,
+  is_evidence tinyint NOT NULL DEFAULT 0,
+  variation_set_id varchar NOT NULL DEFAULT '',
+  somatic tinyint NOT NULL DEFAULT 0,
+  breakpoint_order tinyint,
+  length integer
+);
+
+--
+-- Table: structural_variation_sample
+--
+CREATE TABLE structural_variation_sample (
+  structural_variation_sample_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  structural_variation_id integer NOT NULL,
+  sample_id integer
+);
+
+--
+-- Table: study
+--
+CREATE TABLE study (
+  study_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  source_id integer NOT NULL,
+  name varchar(255),
+  description text,
+  url varchar(255),
+  external_reference varchar(255),
+  study_type varchar(255)
+);
+
+--
+-- Table: submitter_handle
+--
+CREATE TABLE submitter_handle (
+  handle_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  handle varchar(25)
+);
+
+CREATE UNIQUE INDEX handle ON submitter_handle (handle);
+
+--
+-- Table: subsnp_handle
+--
+CREATE TABLE subsnp_handle (
+  subsnp_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  handle varchar(20)
+);
+
+--
+-- Table: subsnp_map
+--
+CREATE TABLE subsnp_map (
+  variation_id integer NOT NULL,
+  subsnp_id integer
+);
+
+--
+-- Table: tagged_variation_feature
+--
+CREATE TABLE tagged_variation_feature (
+  variation_feature_id integer NOT NULL,
+  tagged_variation_feature_id integer,
+  population_id integer NOT NULL
+);
+
+--
+-- Table: tmp_sample_genotype_single_bp
+--
+CREATE TABLE tmp_sample_genotype_single_bp (
+  variation_id integer NOT NULL,
+  subsnp_id integer,
+  allele_1 char(1),
+  allele_2 char(1),
+  sample_id integer NOT NULL
+);
+
+--
+-- Table: transcript_variation
+--
+CREATE TABLE transcript_variation (
+  transcript_variation_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  variation_feature_id integer NOT NULL,
+  feature_stable_id varchar(128),
+  allele_string text,
+  somatic tinyint NOT NULL DEFAULT 0,