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Commit da850074 authored by Patrick Meidl's avatar Patrick Meidl
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put back in missed statement

parent fd59ef99
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...@@ -21,13 +21,14 @@ ALTER TABLE transcript ADD description text; ...@@ -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 t, xref x SET t.description = x.description WHERE t.display_xref_id = x.xref_id;
UPDATE transcript SET description=NULL WHERE description=""; UPDATE transcript SET description=NULL WHERE description="";
# usefull settings for the new tables # 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 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%'; 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 # some vega specific stuff, shouldnt harm anybody else
UPDATE gene SET biotype='unclassified' WHERE biotype = 'Transcript'; UPDATE gene SET biotype='unclassified' WHERE biotype = 'Transcript';
UPDATE gene SET biotype='pseudogene' WHERE biotype = 'Pseudogene'; UPDATE gene SET biotype='pseudogene' WHERE biotype = 'Pseudogene';
UPDATE gene SET biotype='protein_coding', confidence='NOVEL' WHERE biotype = 'Novel_CDS'; 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 ...@@ -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 # new tables regulatory stuff and transcript supporting features
################################################################################ ################################################################################
# #
# Table structure for table 'regulatory_feature' # Table structure for table 'regulatory_feature'
......
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