diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/SQLite/table.sql b/modules/t/test-genome-DBs/homo_sapiens/variation/SQLite/table.sql deleted file mode 100644 index abccb33bd88823930380f68796f67115170d3e16..0000000000000000000000000000000000000000 --- a/modules/t/test-genome-DBs/homo_sapiens/variation/SQLite/table.sql +++ /dev/null @@ -1,784 +0,0 @@ --- --- Created by SQL::Translator::Producer::SQLite --- Created on Fri May 6 15:44:47 2016 --- - -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(255) -); - -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, - 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 text, - 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(255), - allele_2 varchar(255), - sample_id integer -); - --- --- Table: sample_population --- -CREATE TABLE sample_population ( - sample_id integer NOT NULL, - population_id integer NOT NULL -); - --- --- Table: sample_synonym --- -CREATE TABLE sample_synonym ( - synonym_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL, - sample_id integer NOT NULL, - source_id integer NOT NULL, - name varchar(255) -); - --- --- 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: strain_gtype_poly --- -CREATE TABLE strain_gtype_poly ( - variation_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL, - sample_name varchar(100) -); - --- --- 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, - somatic tinyint NOT NULL DEFAULT 0, - breakpoint_order tinyint, - length integer, - variation_set_id varchar NOT NULL DEFAULT '' -); - --- --- 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, - strain_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 NOT NULL, - PRIMARY KEY (variation_id, subsnp_id) -); - --- --- Table: tmp_individual_genotype_single_bp --- -CREATE TABLE tmp_individual_genotype_single_bp ( - variation_id integer NOT NULL, - subsnp_id integer, - allele_1 char(1), - allele_2 char(1), - individual_id integer -); - --- --- 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, - consequence_types varchar, - cds_start integer, - cds_end integer, - cdna_start integer, - cdna_end integer, - translation_start integer, - translation_end integer, - distance_to_transcript integer, - codon_allele_string text, - pep_allele_string text, - hgvs_genomic text, - hgvs_transcript text, - hgvs_protein text, - polyphen_prediction enum, - polyphen_score float, - sift_prediction enum, - sift_score float, - display integer DEFAULT 1 -); - --- --- Table: translation_md5 --- -CREATE TABLE translation_md5 ( - translation_md5_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL, - translation_md5 char(32) NOT NULL -); - -CREATE UNIQUE INDEX md5_idx ON translation_md5 (translation_md5); - --- --- Table: variation --- -CREATE TABLE variation ( - variation_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL, - source_id integer NOT NULL, - name varchar(255), - ancestral_allele varchar(255), - flipped tinyint, - class_attrib_id integer DEFAULT 0, - somatic tinyint NOT NULL DEFAULT 0, - minor_allele varchar(50), - minor_allele_freq float, - minor_allele_count integer, - clinical_significance varchar, - evidence_attribs varchar, - display integer DEFAULT 1 -); - -CREATE UNIQUE INDEX name ON variation (name); - --- --- Table: variation_attrib --- -CREATE TABLE variation_attrib ( - variation_id integer NOT NULL, - attrib_id integer, - value varchar(255) -); - --- --- Table: variation_citation --- -CREATE TABLE variation_citation ( - variation_id integer NOT NULL, - publication_id integer NOT NULL, - PRIMARY KEY (variation_id, publication_id) -); - --- --- Table: variation_feature --- -CREATE TABLE variation_feature ( - variation_feature_id INTEGER PRIMARY KEY AUTOINCREMENT 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, - variation_id integer NOT NULL, - allele_string varchar(50000), - variation_name varchar(255), - map_weight integer NOT NULL, - flags varchar, - source_id integer NOT NULL, - consequence_types varchar NOT NULL DEFAULT 'intergenic_variant', - variation_set_id varchar NOT NULL DEFAULT '', - class_attrib_id integer DEFAULT 0, - somatic tinyint NOT NULL DEFAULT 0, - minor_allele varchar(50), - minor_allele_freq float, - minor_allele_count integer, - alignment_quality double precision, - clinical_significance varchar, - evidence_attribs varchar, - display integer DEFAULT 1 -); - --- --- Table: variation_feature_bak --- -CREATE TABLE variation_feature_bak ( - variation_feature_id integer NOT NULL DEFAULT 0, - seq_region_id integer NOT NULL, - seq_region_start integer NOT NULL, - seq_region_end integer NOT NULL, - seq_region_strand tinyint NOT NULL, - variation_id integer NOT NULL, - allele_string varchar(50000), - variation_name varchar(255), - map_weight integer NOT NULL, - flags varchar, - source_id integer NOT NULL, - validation_status varchar, - consequence_types varchar NOT NULL DEFAULT 'intergenic_variant', - variation_set_id varchar NOT NULL DEFAULT '', - class_attrib_id integer DEFAULT 0, - somatic tinyint NOT NULL DEFAULT 0, - minor_allele varchar(50), - minor_allele_freq float, - minor_allele_count integer, - alignment_quality double precision, - evidence varchar -); - --- --- Table: variation_genename --- -CREATE TABLE variation_genename ( - variation_id integer NOT NULL, - gene_name varchar(255) NOT NULL, - PRIMARY KEY (variation_id, gene_name) -); - --- --- Table: variation_hgvs --- -CREATE TABLE variation_hgvs ( - variation_id integer NOT NULL, - hgvs_name varchar(255) NOT NULL, - PRIMARY KEY (variation_id, hgvs_name) -); - --- --- Table: variation_set --- -CREATE TABLE variation_set ( - variation_set_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL, - name varchar(255), - description text, - short_name_attrib_id integer -); - --- --- Table: variation_set_structural_variation --- -CREATE TABLE variation_set_structural_variation ( - structural_variation_id integer NOT NULL, - variation_set_id integer NOT NULL, - PRIMARY KEY (structural_variation_id, variation_set_id) -); - --- --- Table: variation_set_structure --- -CREATE TABLE variation_set_structure ( - variation_set_super integer NOT NULL, - variation_set_sub integer NOT NULL, - PRIMARY KEY (variation_set_super, variation_set_sub) -); - --- --- Table: variation_set_variation --- -CREATE TABLE variation_set_variation ( - variation_id integer NOT NULL, - variation_set_id integer NOT NULL, - PRIMARY KEY (variation_id, variation_set_id) -); - --- --- Table: variation_synonym --- -CREATE TABLE variation_synonym ( - variation_synonym_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL, - variation_id integer NOT NULL, - subsnp_id integer, - source_id integer NOT NULL, - name varchar(255) -); - -CREATE UNIQUE INDEX name02 ON variation_synonym (name, source_id); - -COMMIT; diff --git a/modules/t/test-genome-DBs/mus_musculus/variation/SQLite/table.sql b/modules/t/test-genome-DBs/mus_musculus/variation/SQLite/table.sql deleted file mode 100644 index 1b9077b9a87a221e580fe93e282f55720ef593a2..0000000000000000000000000000000000000000 --- a/modules/t/test-genome-DBs/mus_musculus/variation/SQLite/table.sql +++ /dev/null @@ -1,747 +0,0 @@ --- --- Created by SQL::Translator::Producer::SQLite --- Created on Fri May 6 15:45:33 2016 --- - -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, - 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: sample_synonym --- -CREATE TABLE sample_synonym ( - synonym_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL, - sample_id integer NOT NULL, - source_id integer NOT NULL, - name varchar(255) -); - --- --- 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: 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, - consequence_types varchar, - cds_start integer, - cds_end integer, - cdna_start integer, - cdna_end integer, - translation_start integer, - translation_end integer, - distance_to_transcript integer, - codon_allele_string text, - pep_allele_string text, - hgvs_genomic text, - hgvs_transcript text, - hgvs_protein text, - polyphen_prediction enum, - sift_prediction enum, - polyphen_score float, - sift_score float, - display integer DEFAULT 1 -); - --- --- Table: translation_md5 --- -CREATE TABLE translation_md5 ( - translation_md5_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL, - translation_md5 char(32) NOT NULL -); - -CREATE UNIQUE INDEX md5_idx ON translation_md5 (translation_md5); - --- --- Table: variation --- -CREATE TABLE variation ( - variation_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL, - source_id integer NOT NULL, - name varchar(255), - ancestral_allele varchar(255), - flipped tinyint, - class_attrib_id integer DEFAULT 0, - somatic tinyint NOT NULL DEFAULT 0, - minor_allele varchar(50), - minor_allele_freq float, - minor_allele_count integer, - clinical_significance varchar, - evidence_attribs varchar, - display integer DEFAULT 1 -); - -CREATE UNIQUE INDEX name ON variation (name); - --- --- Table: variation_attrib --- -CREATE TABLE variation_attrib ( - variation_id integer NOT NULL, - attrib_id integer, - value varchar(255) -); - --- --- Table: variation_citation --- -CREATE TABLE variation_citation ( - variation_id integer NOT NULL, - publication_id integer NOT NULL, - PRIMARY KEY (variation_id, publication_id) -); - --- --- Table: variation_feature --- -CREATE TABLE variation_feature ( - variation_feature_id INTEGER PRIMARY KEY AUTOINCREMENT 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, - variation_id integer NOT NULL, - allele_string varchar(100), - variation_name varchar(255), - map_weight integer NOT NULL, - flags varchar, - source_id integer NOT NULL, - consequence_types varchar NOT NULL DEFAULT 'intergenic_variant', - variation_set_id varchar NOT NULL DEFAULT '', - class_attrib_id integer DEFAULT 0, - somatic tinyint NOT NULL DEFAULT 0, - minor_allele varchar(50), - minor_allele_freq float, - minor_allele_count integer, - alignment_quality double precision, - evidence_attribs varchar, - clinical_significance varchar, - display integer DEFAULT 1 -); - --- --- Table: variation_genename --- -CREATE TABLE variation_genename ( - variation_id integer NOT NULL, - gene_name varchar(255) NOT NULL, - PRIMARY KEY (variation_id, gene_name) -); - --- --- Table: variation_hgvs --- -CREATE TABLE variation_hgvs ( - variation_id integer NOT NULL, - hgvs_name varchar(255) NOT NULL, - PRIMARY KEY (variation_id, hgvs_name) -); - --- --- Table: variation_set --- -CREATE TABLE variation_set ( - variation_set_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL, - name varchar(255), - description text, - short_name_attrib_id integer -); - --- --- Table: variation_set_structural_variation --- -CREATE TABLE variation_set_structural_variation ( - structural_variation_id integer NOT NULL, - variation_set_id integer NOT NULL, - PRIMARY KEY (structural_variation_id, variation_set_id) -); - --- --- Table: variation_set_structure --- -CREATE TABLE variation_set_structure ( - variation_set_super integer NOT NULL, - variation_set_sub integer NOT NULL, - PRIMARY KEY (variation_set_super, variation_set_sub) -); - --- --- Table: variation_set_variation --- -CREATE TABLE variation_set_variation ( - variation_id integer NOT NULL, - variation_set_id integer NOT NULL, - PRIMARY KEY (variation_id, variation_set_id) -); - --- --- Table: variation_synonym --- -CREATE TABLE variation_synonym ( - variation_synonym_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL, - variation_id integer NOT NULL, - subsnp_id integer, - source_id integer NOT NULL, - name varchar(255) -); - -CREATE UNIQUE INDEX name02 ON variation_synonym (name, source_id); - -COMMIT;