def searchFeaturesInDb(
self, startIndex=0, maxResults=None,
referenceName=None, start=None, end=None,
parentId=None, featureTypes=None,
name=None, geneSymbol=None):
"""
Perform a full features query in database.
:param startIndex: int representing first record to return
:param maxResults: int representing number of records to return
:param referenceName: string representing reference name, ex 'chr1'
:param start: int position on reference to start search
:param end: int position on reference to end search >= start
:param parentId: string restrict search by id of parent node.
:param name: match features by name
:param geneSymbol: match features by gene symbol
:return an array of dictionaries, representing the returned data.
"""
# TODO: Refactor out common bits of this and the above count query.
sql, sql_args = self.featuresQuery(
startIndex=startIndex, maxResults=maxResults,
referenceName=referenceName, start=start, end=end,
parentId=parentId, featureTypes=featureTypes,
name=name, geneSymbol=geneSymbol)
sql += sqlite_backend.limitsSql(startIndex, maxResults)
query = self._dbconn.execute(sql, sql_args)
return sqlite_backend.sqliteRowsToDicts(query.fetchall())
def testRowsToDicts(self):
rows = None
with self._db as db:
rows = db.getReadGroupRows()
rowDicts = sqlite_backend.sqliteRowsToDicts(rows)
for rowDict in rowDicts:
self._testRowDict(rowDict)
def testRowsToDicts(self):
rows = None
with self._db as db:
rows = db.getReadGroupRows()
rowDicts = sqlite_backend.sqliteRowsToDicts(rows)
for rowDict in rowDicts:
self._testRowDict(rowDict)
def searchFeaturesInDb(self,
startIndex=0,
maxResults=None,
referenceName=None,
start=None,
end=None,
parentId=None,
featureTypes=None,
name=None,
geneSymbol=None):
"""
Perform a full features query in database.
:param startIndex: int representing first record to return
:param maxResults: int representing number of records to return
:param referenceName: string representing reference name, ex 'chr1'
:param start: int position on reference to start search
:param end: int position on reference to end search >= start
:param parentId: string restrict search by id of parent node.
:param name: match features by name
:param geneSymbol: match features by gene symbol
:return an array of dictionaries, representing the returned data.
"""
# TODO: Refactor out common bits of this and the above count query.
sql, sql_args = self.featuresQuery(startIndex=startIndex,
maxResults=maxResults,
referenceName=referenceName,
start=start,
end=end,
parentId=parentId,
featureTypes=featureTypes,
name=name,
geneSymbol=geneSymbol)
sql += sqlite_backend.limitsSql(startIndex, maxResults)
query = self._dbconn.execute(sql, sql_args)
return sqlite_backend.sqliteRowsToDicts(query.fetchall())
