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comparison cummeRbund_options.py @ 0:587c425b4e76 draft

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Initial commit with version 1.0.0 of the cummeRbund wrapper.
author devteam
date Tue, 23 Dec 2014 15:58:27 -0500
parents
children f3012521ea79
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-1:000000000000 0:587c425b4e76
1 from galaxy import eggs
2 eggs.require( 'SQLAlchemy' )
3 eggs.require( 'pysqlite>=2' )
4 from sqlalchemy import *
5 from sqlalchemy.sql import and_
6 from sqlalchemy import exceptions as sa_exceptions
7 from sqlalchemy.orm import sessionmaker
8 from sqlalchemy.orm import scoped_session
9
10 def get_genes( database_path ):
11 dburi = 'sqlite:///%s' % database_path
12 engine = create_engine( dburi )
13 meta = MetaData( bind=engine )
14 db_session = Session = scoped_session( sessionmaker( bind=engine, autoflush=False, autocommit=True ) )
15 gene_ids = db_session.execute( 'select gene_short_name, gene_id from genes order by gene_short_name' )
16 return [ ( gene_id[ 0 ], gene_id[ 1 ], False ) for gene_id in gene_ids ]
17
18 def get_samples( database_path ):
19 dburi = 'sqlite:///%s' % database_path
20 engine = create_engine( dburi )
21 meta = MetaData( bind=engine )
22 db_session = Session = scoped_session( sessionmaker( bind=engine, autoflush=False, autocommit=True ) )
23 samples = db_session.execute( 'select sample_name from samples order by sample_name' )
24 return [ ( sample[ 0 ], sample[ 0 ], False ) for sample in samples ]