--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cummeRbund_options.py	Tue Dec 23 15:58:27 2014 -0500
@@ -0,0 +1,24 @@
+from galaxy import eggs
+eggs.require( 'SQLAlchemy' )
+eggs.require( 'pysqlite>=2' )
+from sqlalchemy import *
+from sqlalchemy.sql import and_
+from sqlalchemy import exceptions as sa_exceptions
+from sqlalchemy.orm import sessionmaker
+from sqlalchemy.orm import scoped_session
+
+def get_genes( database_path ):
+    dburi = 'sqlite:///%s' % database_path
+    engine = create_engine( dburi )
+    meta = MetaData( bind=engine )
+    db_session = Session = scoped_session( sessionmaker( bind=engine, autoflush=False, autocommit=True ) )
+    gene_ids = db_session.execute( 'select gene_short_name, gene_id from genes order by gene_short_name' )
+    return [ ( gene_id[ 0 ], gene_id[ 1 ], False ) for gene_id in gene_ids ]
+
+def get_samples( database_path ):
+    dburi = 'sqlite:///%s' % database_path
+    engine = create_engine( dburi )
+    meta = MetaData( bind=engine )
+    db_session = Session = scoped_session( sessionmaker( bind=engine, autoflush=False, autocommit=True ) )
+    samples = db_session.execute( 'select sample_name from samples order by sample_name' )
+    return [ ( sample[ 0 ], sample[ 0 ], False ) for sample in samples ]