def getTopLevelFeatures(self, organism):
dolog("getting top level features for " + str(organism))
query = "select f.uniquename,f.feature_id from feature f "
query += "join cvterm on f.type_id = cvterm.cvterm_id "
query += "join featureprop using (feature_id) "
query += "where f.organism_id= "
query += str(organism)
query += " and featureprop.type_id in "
query += " (select cvterm_id from cvterm join cv using (cv_id) where cv.name = 'genedb_misc' and cvterm.name = 'top_level_seq') "
# query += " and f.type_id not in ('432', '1087') "
query += "order by uniquename ";
self.cur.execute(query)
rows = self.cur.fetchall()
features = []
for row in rows:
# print row
feature = Feature(row[0], row[1])
features.append(feature)
return features
def gffTopLevelFeature(gffQueries, feature):
rows = gffQueries.getGFF3View(feature.feature_id)
dolog(feature.uniquename)
feature_ids = []
for r in rows:
feature_ids.append(r[0])
relations = gffQueries.getRelations("objects", feature_ids)
residues = gffQueries.getResidues(feature.feature_id)
if residues == None:
residues = ""
gffFormatter = GFFFormatter(feature, rows, relations, residues)
gffFormatter.parse()
format = gffFormatter.format()
# try to stop leaks...
gffFormatter = None
relations = None
residues = None
return format
