def get_array_id2QC(call_method_id=1, **keywords): """ 2008-04-30 get the array_id 2 QC of calls from simple calling algorithm (call_method_id=1) """ import sys, os sys.stderr.write("Getting array_id2QC ... ") from variation.src.db import Stock_250kDatabase, CallQC db = Stock_250kDatabase(username=keywords['user'], password=keywords['passwd'], host=keywords['hostname'], database=keywords['dbname']) session = db.session array_id2QC = {} for row in session.query(CallQC).list(): if row.call_info_obj.method_id != call_method_id: #simple calling algorithm continue array_id = row.call_info_obj.array_id if array_id in array_id2QC: if row.no_of_non_NA_pairs > array_id2QC[ array_id].no_of_non_NA_pairs: #replace the QC if there are more non-NA pairs array_id2QC[array_id] = row else: array_id2QC[array_id] = row sys.stderr.write("Done.\n") del db return array_id2QC
def _setup_mappers(self, tables, mappers): """Map the database Tables to SQLAlchemy Mapper objects """ Stock_250kDatabase._setup_mappers(tables, mappers) """
def _setup_tables(self, metadata, tables): """Map the database structure to SQLAlchemy Table objects """ Stock_250kDatabase._setup_tables(metadata, tables) """