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