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files.sql
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214 lines (209 loc) · 13.5 KB
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BEGIN TRANSACTION;
CREATE TABLE contig (
id VARCHAR NOT NULL,
PRIMARY KEY (id)
);
INSERT INTO contig VALUES('1');
INSERT INTO contig VALUES('2');
INSERT INTO contig VALUES('3');
INSERT INTO contig VALUES('4');
INSERT INTO contig VALUES('5');
INSERT INTO contig VALUES('6');
INSERT INTO contig VALUES('7');
INSERT INTO contig VALUES('8');
INSERT INTO contig VALUES('9');
INSERT INTO contig VALUES('10');
INSERT INTO contig VALUES('11');
INSERT INTO contig VALUES('12');
INSERT INTO contig VALUES('13');
INSERT INTO contig VALUES('14');
INSERT INTO contig VALUES('15');
INSERT INTO contig VALUES('16');
INSERT INTO contig VALUES('17');
INSERT INTO contig VALUES('18');
INSERT INTO contig VALUES('19');
INSERT INTO contig VALUES('20');
INSERT INTO contig VALUES('21');
INSERT INTO contig VALUES('22');
INSERT INTO contig VALUES('X');
INSERT INTO contig VALUES('Y');
INSERT INTO contig VALUES('MT');
CREATE TABLE alias (
id VARCHAR NOT NULL,
contig_id VARCHAR,
PRIMARY KEY (id),
FOREIGN KEY(contig_id) REFERENCES contig (id)
);
INSERT INTO alias VALUES('chr1','1');
INSERT INTO alias VALUES('chr2','2');
INSERT INTO alias VALUES('chr3','3');
INSERT INTO alias VALUES('chr4','4');
INSERT INTO alias VALUES('chr5','5');
INSERT INTO alias VALUES('chr6','6');
INSERT INTO alias VALUES('chr7','7');
INSERT INTO alias VALUES('chr8','8');
INSERT INTO alias VALUES('chr9','9');
INSERT INTO alias VALUES('chr10','10');
INSERT INTO alias VALUES('chr11','11');
INSERT INTO alias VALUES('chr12','12');
INSERT INTO alias VALUES('chr13','13');
INSERT INTO alias VALUES('chr14','14');
INSERT INTO alias VALUES('chr15','15');
INSERT INTO alias VALUES('chr16','16');
INSERT INTO alias VALUES('chr17','17');
INSERT INTO alias VALUES('chr18','18');
INSERT INTO alias VALUES('chr19','19');
INSERT INTO alias VALUES('chr20','20');
INSERT INTO alias VALUES('chr21','21');
INSERT INTO alias VALUES('chr22','22');
INSERT INTO alias VALUES('chrX','X');
INSERT INTO alias VALUES('chrY','Y');
INSERT INTO alias VALUES('chrMT','MT');
INSERT INTO alias VALUES('Chr1','1');
INSERT INTO alias VALUES('Chr2','2');
INSERT INTO alias VALUES('Chr3','3');
INSERT INTO alias VALUES('Chr4','4');
INSERT INTO alias VALUES('Chr5','5');
INSERT INTO alias VALUES('Chr6','6');
INSERT INTO alias VALUES('Chr7','7');
INSERT INTO alias VALUES('Chr8','8');
INSERT INTO alias VALUES('Chr9','9');
INSERT INTO alias VALUES('Chr10','10');
INSERT INTO alias VALUES('Chr11','11');
INSERT INTO alias VALUES('Chr12','12');
INSERT INTO alias VALUES('Chr13','13');
INSERT INTO alias VALUES('Chr14','14');
INSERT INTO alias VALUES('Chr15','15');
INSERT INTO alias VALUES('Chr16','16');
INSERT INTO alias VALUES('Chr17','17');
INSERT INTO alias VALUES('Chr18','18');
INSERT INTO alias VALUES('Chr19','19');
INSERT INTO alias VALUES('Chr20','20');
INSERT INTO alias VALUES('Chr21','21');
INSERT INTO alias VALUES('Chr22','22');
INSERT INTO alias VALUES('ChrX','X');
INSERT INTO alias VALUES('ChrY','Y');
INSERT INTO alias VALUES('ChrMT','MT');
INSERT INTO alias VALUES('x','X');
INSERT INTO alias VALUES('y','Y');
INSERT INTO alias VALUES('mt','MT');
INSERT INTO alias VALUES('M','MT');
INSERT INTO alias VALUES('chrM','MT');
INSERT INTO alias VALUES('ChrM','MT');
CREATE TABLE variantfile (
id VARCHAR NOT NULL,
drs_object_id VARCHAR,
indexed INTEGER,
chr_prefix VARCHAR,
reference_genome VARCHAR,
PRIMARY KEY (id)
-- FOREIGN KEY(drs_object_id) REFERENCES drs_object (id)
);
CREATE TABLE pos_bucket (
id SERIAL PRIMARY KEY,
pos_bucket_id INTEGER NOT NULL,
contig_id VARCHAR,
FOREIGN KEY(contig_id) REFERENCES contig (id)
);
CREATE TABLE header (
id SERIAL PRIMARY KEY,
text VARCHAR NOT NULL
);
CREATE TABLE contig_variantfile_association (
contig_id VARCHAR NOT NULL,
variantfile_id VARCHAR NOT NULL,
PRIMARY KEY (contig_id, variantfile_id),
FOREIGN KEY(contig_id) REFERENCES contig (id),
FOREIGN KEY(variantfile_id) REFERENCES variantfile (id)
);
CREATE TABLE header_variantfile_association (
header_id INTEGER NOT NULL,
variantfile_id VARCHAR NOT NULL,
PRIMARY KEY (header_id, variantfile_id),
FOREIGN KEY(header_id) REFERENCES header (id),
FOREIGN KEY(variantfile_id) REFERENCES variantfile (id)
);
CREATE TABLE pos_bucket_variantfile_association (
pos_bucket_id INTEGER NOT NULL,
variantfile_id VARCHAR NOT NULL,
bucket_count INTEGER NOT NULL DEFAULT 0,
PRIMARY KEY (pos_bucket_id, variantfile_id),
FOREIGN KEY(pos_bucket_id) REFERENCES pos_bucket (id),
FOREIGN KEY(variantfile_id) REFERENCES variantfile (id)
);
CREATE TABLE sample (
id SERIAL PRIMARY KEY,
sample_id VARCHAR,
variantfile_id VARCHAR,
FOREIGN KEY(variantfile_id) REFERENCES variantfile (id)
);
-- ncbirefseq table modified from https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/
-- field example description
-- reference_genome hg38 Reference genome build
-- gene_name DDX11L1 varchar(255) values Gene name from http://www.genenames.org/
-- transcript_name NR_046018.2 Transcript name from NCBI RefSeq
-- contig 1 Reference sequence chromosome or scaffold
-- start 11873 Transcription start position (or end position for minus strand item)
-- endpos 14409 Transcription end position (or start position for minus strand item)
CREATE TABLE ncbirefseq (
id SERIAL PRIMARY KEY,
reference_genome varchar(10) NOT NULL,
gene_name varchar(255) NOT NULL,
transcript_name varchar(255) NOT NULL,
contig varchar(25) NOT NULL,
start int NOT NULL,
endpos int NOT NULL,
UNIQUE(reference_genome, contig, gene_name, transcript_name)
);
-- insert reference sequences for chromosomes: ncbi reference name is in transcript name, but gene name is empty
INSERT INTO ncbirefseq (reference_genome, transcript_name, contig, start, endpos, gene_name) VALUES ('hg38', 'NC_000001.11', '1', 0, 0, '') ON CONFLICT DO NOTHING;
INSERT INTO ncbirefseq (reference_genome, transcript_name, contig, start, endpos, gene_name) VALUES ('hg38', 'NC_000002.12', '2', 0, 0, '') ON CONFLICT DO NOTHING;
INSERT INTO ncbirefseq (reference_genome, transcript_name, contig, start, endpos, gene_name) VALUES ('hg38', 'NC_000003.12', '3', 0, 0, '') ON CONFLICT DO NOTHING;
INSERT INTO ncbirefseq (reference_genome, transcript_name, contig, start, endpos, gene_name) VALUES ('hg38', 'NC_000004.12', '4', 0, 0, '') ON CONFLICT DO NOTHING;
INSERT INTO ncbirefseq (reference_genome, transcript_name, contig, start, endpos, gene_name) VALUES ('hg38', 'NC_000005.10', '5', 0, 0, '') ON CONFLICT DO NOTHING;
INSERT INTO ncbirefseq (reference_genome, transcript_name, contig, start, endpos, gene_name) VALUES ('hg38', 'NC_000006.12', '6', 0, 0, '') ON CONFLICT DO NOTHING;
INSERT INTO ncbirefseq (reference_genome, transcript_name, contig, start, endpos, gene_name) VALUES ('hg38', 'NC_000007.14', '7', 0, 0, '') ON CONFLICT DO NOTHING;
INSERT INTO ncbirefseq (reference_genome, transcript_name, contig, start, endpos, gene_name) VALUES ('hg38', 'NC_000008.11', '8', 0, 0, '') ON CONFLICT DO NOTHING;
INSERT INTO ncbirefseq (reference_genome, transcript_name, contig, start, endpos, gene_name) VALUES ('hg38', 'NC_000009.12', '9', 0, 0, '') ON CONFLICT DO NOTHING;
INSERT INTO ncbirefseq (reference_genome, transcript_name, contig, start, endpos, gene_name) VALUES ('hg38', 'NC_000010.11', '10', 0, 0, '') ON CONFLICT DO NOTHING;
INSERT INTO ncbirefseq (reference_genome, transcript_name, contig, start, endpos, gene_name) VALUES ('hg38', 'NC_000011.10', '11', 0, 0, '') ON CONFLICT DO NOTHING;
INSERT INTO ncbirefseq (reference_genome, transcript_name, contig, start, endpos, gene_name) VALUES ('hg38', 'NC_000012.12', '12', 0, 0, '') ON CONFLICT DO NOTHING;
INSERT INTO ncbirefseq (reference_genome, transcript_name, contig, start, endpos, gene_name) VALUES ('hg38', 'NC_000013.11', '13', 0, 0, '') ON CONFLICT DO NOTHING;
INSERT INTO ncbirefseq (reference_genome, transcript_name, contig, start, endpos, gene_name) VALUES ('hg38', 'NC_000014.9', '14', 0, 0, '') ON CONFLICT DO NOTHING;
INSERT INTO ncbirefseq (reference_genome, transcript_name, contig, start, endpos, gene_name) VALUES ('hg38', 'NC_000015.10', '15', 0, 0, '') ON CONFLICT DO NOTHING;
INSERT INTO ncbirefseq (reference_genome, transcript_name, contig, start, endpos, gene_name) VALUES ('hg38', 'NC_000016.10', '16', 0, 0, '') ON CONFLICT DO NOTHING;
INSERT INTO ncbirefseq (reference_genome, transcript_name, contig, start, endpos, gene_name) VALUES ('hg38', 'NC_000017.11', '17', 0, 0, '') ON CONFLICT DO NOTHING;
INSERT INTO ncbirefseq (reference_genome, transcript_name, contig, start, endpos, gene_name) VALUES ('hg38', 'NC_000018.10', '18', 0, 0, '') ON CONFLICT DO NOTHING;
INSERT INTO ncbirefseq (reference_genome, transcript_name, contig, start, endpos, gene_name) VALUES ('hg38', 'NC_000019.10', '19', 0, 0, '') ON CONFLICT DO NOTHING;
INSERT INTO ncbirefseq (reference_genome, transcript_name, contig, start, endpos, gene_name) VALUES ('hg38', 'NC_000020.11', '20', 0, 0, '') ON CONFLICT DO NOTHING;
INSERT INTO ncbirefseq (reference_genome, transcript_name, contig, start, endpos, gene_name) VALUES ('hg38', 'NC_000021.9', '21', 0, 0, '') ON CONFLICT DO NOTHING;
INSERT INTO ncbirefseq (reference_genome, transcript_name, contig, start, endpos, gene_name) VALUES ('hg38', 'NC_000022.11', '22', 0, 0, '') ON CONFLICT DO NOTHING;
INSERT INTO ncbirefseq (reference_genome, transcript_name, contig, start, endpos, gene_name) VALUES ('hg38', 'NC_000023.11', 'X', 0, 0, '') ON CONFLICT DO NOTHING;
INSERT INTO ncbirefseq (reference_genome, transcript_name, contig, start, endpos, gene_name) VALUES ('hg38', 'NC_000024.10', 'Y', 0, 0, '') ON CONFLICT DO NOTHING;
INSERT INTO ncbirefseq (reference_genome, transcript_name, contig, start, endpos, gene_name) VALUES ('hg38', 'NC_012920.1', 'MT', 0, 0, '') ON CONFLICT DO NOTHING;
INSERT INTO ncbirefseq (reference_genome, transcript_name, contig, start, endpos, gene_name) VALUES ('hg37', 'NC_000001.10', '1', 0, 0, '') ON CONFLICT DO NOTHING;
INSERT INTO ncbirefseq (reference_genome, transcript_name, contig, start, endpos, gene_name) VALUES ('hg37', 'NC_000002.11', '2', 0, 0, '') ON CONFLICT DO NOTHING;
INSERT INTO ncbirefseq (reference_genome, transcript_name, contig, start, endpos, gene_name) VALUES ('hg37', 'NC_000003.11', '3', 0, 0, '') ON CONFLICT DO NOTHING;
INSERT INTO ncbirefseq (reference_genome, transcript_name, contig, start, endpos, gene_name) VALUES ('hg37', 'NC_000004.11', '4', 0, 0, '') ON CONFLICT DO NOTHING;
INSERT INTO ncbirefseq (reference_genome, transcript_name, contig, start, endpos, gene_name) VALUES ('hg37', 'NC_000005.9', '5', 0, 0, '') ON CONFLICT DO NOTHING;
INSERT INTO ncbirefseq (reference_genome, transcript_name, contig, start, endpos, gene_name) VALUES ('hg37', 'NC_000006.11', '6', 0, 0, '') ON CONFLICT DO NOTHING;
INSERT INTO ncbirefseq (reference_genome, transcript_name, contig, start, endpos, gene_name) VALUES ('hg37', 'NC_000007.13', '7', 0, 0, '') ON CONFLICT DO NOTHING;
INSERT INTO ncbirefseq (reference_genome, transcript_name, contig, start, endpos, gene_name) VALUES ('hg37', 'NC_000008.10', '8', 0, 0, '') ON CONFLICT DO NOTHING;
INSERT INTO ncbirefseq (reference_genome, transcript_name, contig, start, endpos, gene_name) VALUES ('hg37', 'NC_000009.11', '9', 0, 0, '') ON CONFLICT DO NOTHING;
INSERT INTO ncbirefseq (reference_genome, transcript_name, contig, start, endpos, gene_name) VALUES ('hg37', 'NC_000010.10', '10', 0, 0, '') ON CONFLICT DO NOTHING;
INSERT INTO ncbirefseq (reference_genome, transcript_name, contig, start, endpos, gene_name) VALUES ('hg37', 'NC_000011.9', '11', 0, 0, '') ON CONFLICT DO NOTHING;
INSERT INTO ncbirefseq (reference_genome, transcript_name, contig, start, endpos, gene_name) VALUES ('hg37', 'NC_000012.11', '12', 0, 0, '') ON CONFLICT DO NOTHING;
INSERT INTO ncbirefseq (reference_genome, transcript_name, contig, start, endpos, gene_name) VALUES ('hg37', 'NC_000013.10', '13', 0, 0, '') ON CONFLICT DO NOTHING;
INSERT INTO ncbirefseq (reference_genome, transcript_name, contig, start, endpos, gene_name) VALUES ('hg37', 'NC_000014.8', '14', 0, 0, '') ON CONFLICT DO NOTHING;
INSERT INTO ncbirefseq (reference_genome, transcript_name, contig, start, endpos, gene_name) VALUES ('hg37', 'NC_000015.9', '15', 0, 0, '') ON CONFLICT DO NOTHING;
INSERT INTO ncbirefseq (reference_genome, transcript_name, contig, start, endpos, gene_name) VALUES ('hg37', 'NC_000016.9', '16', 0, 0, '') ON CONFLICT DO NOTHING;
INSERT INTO ncbirefseq (reference_genome, transcript_name, contig, start, endpos, gene_name) VALUES ('hg37', 'NC_000017.10', '17', 0, 0, '') ON CONFLICT DO NOTHING;
INSERT INTO ncbirefseq (reference_genome, transcript_name, contig, start, endpos, gene_name) VALUES ('hg37', 'NC_000018.9', '18', 0, 0, '') ON CONFLICT DO NOTHING;
INSERT INTO ncbirefseq (reference_genome, transcript_name, contig, start, endpos, gene_name) VALUES ('hg37', 'NC_000019.9', '19', 0, 0, '') ON CONFLICT DO NOTHING;
INSERT INTO ncbirefseq (reference_genome, transcript_name, contig, start, endpos, gene_name) VALUES ('hg37', 'NC_000020.10', '20', 0, 0, '') ON CONFLICT DO NOTHING;
INSERT INTO ncbirefseq (reference_genome, transcript_name, contig, start, endpos, gene_name) VALUES ('hg37', 'NC_000021.8', '21', 0, 0, '') ON CONFLICT DO NOTHING;
INSERT INTO ncbirefseq (reference_genome, transcript_name, contig, start, endpos, gene_name) VALUES ('hg37', 'NC_000022.10', '22', 0, 0, '') ON CONFLICT DO NOTHING;
INSERT INTO ncbirefseq (reference_genome, transcript_name, contig, start, endpos, gene_name) VALUES ('hg37', 'NC_000023.10', 'X', 0, 0, '') ON CONFLICT DO NOTHING;
INSERT INTO ncbirefseq (reference_genome, transcript_name, contig, start, endpos, gene_name) VALUES ('hg37', 'NC_000024.9', 'Y', 0, 0, '') ON CONFLICT DO NOTHING;
INSERT INTO ncbirefseq (reference_genome, transcript_name, contig, start, endpos, gene_name) VALUES ('hg37', 'NC_012920.1', 'MT', 0, 0, '') ON CONFLICT DO NOTHING;
COMMIT;