# Written (W) 2008 Fabio De Bona
# Copyright (C) 2008 Max-Planck-Society
-
#
# This file contains the main interface to the QPalma pipeline.
#
from optparse import OptionParser
-
-from qpalma.gridtools import *
-
+from qpalma.gridtools import ApproximationTask,PreprocessingTask
+from qpalma.gridtools import AlignmentTask,PostprocessingTask
def create_option_parser():
parser = OptionParser()
- setting up the different pipeline modules
- run the experiment and report the results
-
"""
- # Before creating a candidate spliced read dataset we have to first filter
- # the matches from the first seed finding run.
+ def __init__(self):
+ """
+ """
+ parser = create_option_parser()
+ (options, args) = parser.parse_args()
+
+
+ def run(self):
+
+ # Before creating a candidate spliced read dataset we have to first filter
+ # the matches from the first seed finding run.
- grid_heuristic()
+ grid_heuristic()
- # approx_task = ApproximationTask(...)
- # approx_task.createJobs()
- # approx_task.submit()
- # approx_task.checkIfTaskFinished()
+ # approx_task = ApproximationTask(...)
+ # approx_task.createJobs()
+ # approx_task.submit()
+ # approx_task.checkIfTaskFinished()
- # After filtering combine the filtered matches from the first run and the
- # found matches from the second run to a full dataset
+ # After filtering combine the filtered matches from the first run and the
+ # found matches from the second run to a full dataset
- createNewDataset
-
- # pre_task = PreprocessingTask(...)
- # pre_task.createJobs()
- # pre_task.submit()
+ createNewDataset
+
+ # pre_task = PreprocessingTask(...)
+ # pre_task.createJobs()
+ # pre_task.submit()
- # Now that we have a dataset we can perform the accurate alignments for this
- # data
+ # Now that we have a dataset we can perform the accurate alignments for this
+ # data
- grid_predict()
+ grid_predict()
- # align_task = AlignmentTask(...)
- # align_task.createJobs()
- # align_task.submit()
+ # align_task = AlignmentTask(...)
+ # align_task.createJobs()
+ # align_task.submit()
- # The results of the above alignment step can be converted to a data format
- # needed for further postprocessing
+ # The results of the above alignment step can be converted to a data format
+ # needed for further postprocessing
- grid_alignment()
+ grid_alignment()
- # post_task = PostprocessingTask(...)
- # post_task.createJobs()
- # post_task.submit()
+ # post_task = PostprocessingTask(...)
+ # post_task.createJobs()
+ # post_task.submit()
if __name__ == '__main__':
- parser = create_option_parser()
- (options, args) = parser.parse_args()
+ system_obj = System()
+ system_obj.run()