[Gmod-schema-cmts] schema/chado/modules/sequence/gff-bridge sequence-gff-views.sql, 1.13, 1.14

[Scott C. <sco...@us...>]

Update of /cvsroot/gmod/schema/chado/modules/sequence/gff-bridge
In directory sc8-pr-cvs2.sourceforge.net:/tmp/cvs-serv18588

Modified Files:
	sequence-gff-views.sql 
Log Message:
adding in Olivier's suggestion to include Target and Derives_from attributes in the gff3atts view


Index: sequence-gff-views.sql
===================================================================
RCS file: /cvsroot/gmod/schema/chado/modules/sequence/gff-bridge/sequence-gff-views.sql,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** sequence-gff-views.sql	1 Jun 2006 17:23:22 -0000	1.13
--- sequence-gff-views.sql	3 Nov 2006 19:42:27 -0000	1.14
***************
*** 50,56 ****
  SELECT feature_id, 
        'Ontology_term' AS type, 
!       CASE WHEN db.name like '%Gene Ontology%'    THEN 'GO:'||dbx.accession
!            WHEN db.name like 'Sequence Ontology%' THEN 'SO:'||dbx.accession
!            ELSE                            CAST(db.name||':'||dbx.accession AS varchar)
        END 
  FROM cvterm s, dbxref dbx, feature_cvterm fs, db
--- 50,56 ----
  SELECT feature_id, 
        'Ontology_term' AS type, 
!       CASE WHEN db.name like '%Gene Ontology%'    THEN 'GO:'|| dbx.accession
!            WHEN db.name like 'Sequence Ontology%' THEN 'SO:'|| dbx.accession
!            ELSE                            CAST(db.name||':'|| dbx.accession AS varchar)
        END 
  FROM cvterm s, dbxref dbx, feature_cvterm fs, db
***************
*** 58,62 ****
        db.db_id = dbx.db_id 
  UNION ALL
! SELECT feature_id, 'Dbxref' AS type, d.name || ':' || s.accession AS attribute
  FROM dbxref s, feature_dbxref fs, db d
  WHERE fs.dbxref_id = s.dbxref_id and s.db_id = d.db_id and
--- 58,63 ----
        db.db_id = dbx.db_id 
  UNION ALL
! SELECT feature_id, 'Dbxref' AS type, d.name || ':' || s.accession AS
! attribute
  FROM dbxref s, feature_dbxref fs, db d
  WHERE fs.dbxref_id = s.dbxref_id and s.db_id = d.db_id and
***************
*** 72,82 ****
  WHERE fp.type_id = cv.cvterm_id
  UNION ALL
! SELECT feature_id, 'pub' AS type, s.series_name || ':' || s.title AS attribute
  FROM pub s, feature_pub fs
  WHERE fs.pub_id = s.pub_id
  UNION ALL
! SELECT fr.subject_id as feature_id, 'Parent' as type,  parent.uniquename as attribute
  FROM feature_relationship fr, feature parent
! WHERE  fr.object_id=parent.feature_id
  UNION ALL
  SELECT feature_id, 'ID' as type, uniquename as attribute
--- 73,98 ----
  WHERE fp.type_id = cv.cvterm_id
  UNION ALL
! SELECT feature_id, 'pub' AS type, s.series_name || ':' || s.title AS
! attribute
  FROM pub s, feature_pub fs
  WHERE fs.pub_id = s.pub_id
  UNION ALL
! SELECT fr.subject_id as feature_id, 'Parent' as type,  parent.uniquename
! as attribute
  FROM feature_relationship fr, feature parent
! WHERE  fr.object_id=parent.feature_id AND fr.type_id = (SELECT cvterm_id
! FROM cvterm WHERE name='part_of')
! UNION ALL
! SELECT fr.subject_id as feature_id, 'Derived_from' as type,
! parent.uniquename as attribute
! FROM feature_relationship fr, feature parent
! WHERE  fr.object_id=parent.feature_id AND fr.type_id = (SELECT cvterm_id
! FROM cvterm WHERE name='derives_from')
! UNION ALL
! SELECT fl.feature_id, 'Target' as type, target.name || ' ' || fl.fmin+1
! || ' ' || fl.fmax || ' ' || fl.strand as attribute
! FROM featureloc fl, feature target
! WHERE fl.srcfeature_id=target.feature_id
!         AND fl.rank != 0
  UNION ALL
  SELECT feature_id, 'ID' as type, uniquename as attribute
***************
*** 84,88 ****
  WHERE type_id NOT IN (SELECT cvterm_id FROM cvterm WHERE name='CDS')
  UNION ALL
! SELECT feature_id, 'chado_feature_id' as type, CAST(feature_id AS varchar) as attribute
  FROM feature
  UNION ALL
--- 100,105 ----
  WHERE type_id NOT IN (SELECT cvterm_id FROM cvterm WHERE name='CDS')
  UNION ALL
! SELECT feature_id, 'chado_feature_id' as type, CAST(feature_id AS
! varchar) as attribute
  FROM feature
  UNION ALL