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comparison cummeRbund_options.py @ 2:ac2ebc60ef5d draft

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Uploaded corrected dynamic options
author devteam
date Mon, 16 Mar 2015 15:43:02 -0400
parents f3012521ea79
children c3b54a4b7741
comparison
equal deleted inserted replaced
1:f3012521ea79 2:ac2ebc60ef5d
1 from galaxy import eggs 1 import sqlite3
2 eggs.require( 'SQLAlchemy' )
3 eggs.require( 'pysqlite>=2' )
4 from sqlalchemy import *
5 from sqlalchemy.sql import and_
6 from sqlalchemy.orm import sessionmaker
7 from sqlalchemy.orm import scoped_session
8 2
9 def get_genes( database_path ): 3 def get_genes( database_path ):
10 dburi = 'sqlite:///%s' % database_path 4 conn = sqlite3.connect( database_path )
11 engine = create_engine( dburi ) 5 gene_ids = conn.execute( 'SELECT gene_short_name, gene_id FROM genes ORDER BY gene_short_name' )
12 meta = MetaData( bind=engine )
13 db_session = Session = scoped_session( sessionmaker( bind=engine, autoflush=False, autocommit=True ) )
14 gene_ids = db_session.execute( 'select gene_short_name, gene_id from genes order by gene_short_name' )
15 return [ ( gene_id[ 0 ], gene_id[ 1 ], False ) for gene_id in gene_ids ] 6 return [ ( gene_id[ 0 ], gene_id[ 1 ], False ) for gene_id in gene_ids ]
16 7
17 def get_samples( database_path ): 8 def get_samples( database_path ):
18 dburi = 'sqlite:///%s' % database_path 9 conn = sqlite3.connect( database_path )
19 engine = create_engine( dburi ) 10 samples = conn.execute( 'SELECT sample_name FROM samples ORDER BY sample_name' )
20 meta = MetaData( bind=engine )
21 db_session = Session = scoped_session( sessionmaker( bind=engine, autoflush=False, autocommit=True ) )
22 samples = db_session.execute( 'select sample_name from samples order by sample_name' )
23 return [ ( sample[ 0 ], sample[ 0 ], False ) for sample in samples ] 11 return [ ( sample[ 0 ], sample[ 0 ], False ) for sample in samples ]