diff --git a/sql/patch_30_31.sql b/sql/patch_30_31.sql index b8f2a0b75622946892e09144e97b19cc93761ead..96806cbe43b85698f6c1053e766fb5f6a34bf2b4 100644 --- a/sql/patch_30_31.sql +++ b/sql/patch_30_31.sql @@ -21,13 +21,14 @@ ALTER TABLE transcript ADD description text; UPDATE transcript t, xref x SET t.description = x.description WHERE t.display_xref_id = x.xref_id; UPDATE transcript SET description=NULL WHERE description=""; + # usefull settings for the new tables +UPDATE gene SET biotype='protein_coding' WHERE biotype = 'ensembl'; UPDATE gene g, xref x, external_db ed SET g.confidence='KNOWN' WHERE g.display_xref_id = x.xref_id and x.external_db_id = ed.external_db_id and g.display_xref_id != 0 and ed.status like 'KNOWN%'; UPDATE transcript t, xref x, external_db ed SET t.confidence='KNOWN' WHERE t.display_xref_id = x.xref_id and x.external_db_id = ed.external_db_id and t.display_xref_id != 0 and ed.status like 'KNOWN%'; # some vega specific stuff, shouldnt harm anybody else - UPDATE gene SET biotype='unclassified' WHERE biotype = 'Transcript'; UPDATE gene SET biotype='pseudogene' WHERE biotype = 'Pseudogene'; UPDATE gene SET biotype='protein_coding', confidence='NOVEL' WHERE biotype = 'Novel_CDS'; @@ -50,6 +51,7 @@ UPDATE transcript t, gene g SET t.biotype = g.biotype WHERE g.gene_id = t.gene_i # new tables regulatory stuff and transcript supporting features + ################################################################################ # # Table structure for table 'regulatory_feature'