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annotate cummeRbund_options.py @ 1:f3012521ea79 draft

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Uploaded fixed cummeRbund_options.py
author devteam
date Fri, 13 Mar 2015 15:30:17 -0400
parents 587c425b4e76
children ac2ebc60ef5d
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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
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2 eggs.require( 'SQLAlchemy' )
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3 eggs.require( 'pysqlite>=2' )
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4 from sqlalchemy import *
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5 from sqlalchemy.sql import and_
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6 from sqlalchemy.orm import sessionmaker
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7 from sqlalchemy.orm import scoped_session
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9 def get_genes( database_path ):
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10 dburi = 'sqlite:///%s' % database_path
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11 engine = create_engine( dburi )
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12 meta = MetaData( bind=engine )
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13 db_session = Session = scoped_session( sessionmaker( bind=engine, autoflush=False, autocommit=True ) )
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14 gene_ids = db_session.execute( 'select gene_short_name, gene_id from genes order by gene_short_name' )
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15 return [ ( gene_id[ 0 ], gene_id[ 1 ], False ) for gene_id in gene_ids ]
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16
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17 def get_samples( database_path ):
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18 dburi = 'sqlite:///%s' % database_path
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19 engine = create_engine( dburi )
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20 meta = MetaData( bind=engine )
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21 db_session = Session = scoped_session( sessionmaker( bind=engine, autoflush=False, autocommit=True ) )
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22 samples = db_session.execute( 'select sample_name from samples order by sample_name' )
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23 return [ ( sample[ 0 ], sample[ 0 ], False ) for sample in samples ]