diff schema/gafa.sql @ 6:c15476d4271c draft

planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/ commit af1fd308dde99cf40a9422c53dc680932be3765d

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/schema/gafa.sql	Tue Mar 20 11:06:51 2018 -0400
@@ -0,0 +1,25 @@
+CREATE TABLE meta (
+        version VARCHAR PRIMARY KEY NOT NULL);
+CREATE TABLE gene (
+        gene_id VARCHAR PRIMARY KEY NOT NULL,
+        gene_symbol VARCHAR,
+        species VARCHAR NOT NULL,
+        gene_json VARCHAR NOT NULL);
+CREATE INDEX gene_symbol_index ON gene (gene_symbol);
+CREATE TABLE transcript (
+        transcript_id VARCHAR PRIMARY KEY NOT NULL,
+        protein_id VARCHAR UNIQUE,
+        protein_sequence VARCHAR,
+        gene_id VARCHAR NOT NULL REFERENCES gene(gene_id));
+CREATE VIEW transcript_species as
+        SELECT transcript_id, species 
+        FROM transcript JOIN gene
+        ON transcript.gene_id = gene.gene_id;
+CREATE TABLE gene_family (
+        gene_family_id INTEGER PRIMARY KEY,
+        gene_tree VARCHAR NOT NULL);
+CREATE TABLE gene_family_member (
+        gene_family_id INTEGER NOT NULL REFERENCES gene_family(gene_family_id),
+        protein_id VARCHAR KEY NOT NULL REFERENCES transcript(protein_id),
+        protein_alignment VARCHAR NOT NULL,
+        PRIMARY KEY (gene_family_id, protein_id));