Mercurial > repos > devteam > cummerbund
view cummeRbund_options.py @ 0:587c425b4e76 draft
Initial commit with version 1.0.0 of the cummeRbund wrapper.
author | devteam |
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date | Tue, 23 Dec 2014 15:58:27 -0500 |
parents | |
children | f3012521ea79 |
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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 ]