Mercurial > repos > devteam > cummerbund_to_tabular
changeset 1:36f917aa4b60 draft
Uploaded corrected script
| author | devteam |
|---|---|
| date | Mon, 16 Mar 2015 15:43:38 -0400 |
| parents | 648c27c78eed |
| children | 0761bbc0a4e7 |
| files | cummerbund_to_tabular.py cummerbund_to_tabular.xml |
| diffstat | 2 files changed, 3 insertions(+), 14 deletions(-) [+] |
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--- a/cummerbund_to_tabular.py Tue Dec 23 16:01:24 2014 -0500 +++ b/cummerbund_to_tabular.py Mon Mar 16 15:43:38 2015 -0400 @@ -2,19 +2,16 @@ import argparse import sys import string +import sqlite3 -from galaxy.model.orm import * import logging -from galaxy import eggs -eggs.require('SQLAlchemy') -import sqlalchemy class CummerbundParser(object): def __init__(self, opts): self.cummerbund_db = opts.filename - self.__connect_database() + self.session = sqlite3.connect( os.path.abspath( self.cummerbund_db ) ) def generate_file( self, table ): if hasattr( self, table ): @@ -23,14 +20,6 @@ else: print 'Table %s is not supported or does not exist.' % table - def __connect_database( self ): - database_connection = 'sqlite:///%s' % os.path.abspath( self.cummerbund_db ) - # Initialize the database connection. - engine = create_engine( database_connection ) - meta = MetaData( bind=engine ) - sa_sesssion = Session = scoped_session( sessionmaker( bind=engine, autoflush=False, autocommit=True ) ) - self.session = sa_sesssion - def __write_line(self, line): columns = [] for col in line:
--- a/cummerbund_to_tabular.xml Tue Dec 23 16:01:24 2014 -0500 +++ b/cummerbund_to_tabular.xml Mon Mar 16 15:43:38 2015 -0400 @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="cummerbund_to_cuffdiff" name="Extract CuffDiff" version="1.0.0"> +<tool id="cummerbund_to_cuffdiff" name="Extract CuffDiff" version="1.0.1"> <description>tabular files from a cummeRbund database</description> <command interpreter="python"><![CDATA[ cummerbund_to_tabular.py --file ${input_database}