+ added convenient script
[qpalma.git] / tools / run_specific_scripts / transcriptome_analysis / createNewDataset.py
index 42ed713..19cb0c7 100644 (file)
@@ -2,24 +2,29 @@
 # -*- coding: utf-8 -*-
 
 import os.path
+import cProfile
 
-import qpalma.Configuration as Conf
 from compile_dataset import DatasetGenerator
 
-jp = os.path.join
 
-#working_dir='/fml/ag-raetsch/home/fabio/tmp/transcriptome_data'
-#working_dir='/fml/ag-raetsch/home/fabio/tmp/transcriptome_data'
+def run():
+   jp = os.path.join
 
-working_dir='/fml/ag-raetsch/share/projects/qpalma/solexa/new_run2/mapping/spliced'
+   main_dir = '/fml/ag-raetsch/home/fabio/tmp/vmatch_evaluation/main'
 
+   #spliced_dir = '/fml/ag-raetsch/home/fabio/tmp/vmatch_evaluation/spliced_1'
+   #result_dir = '/fml/ag-raetsch/home/fabio/tmp/vmatch_evaluation/spliced_1/dataset'
 
-result_dir='/fml/ag-raetsch/home/fabio/tmp/sandbox'
+   spliced_dir = '/fml/ag-raetsch/home/fabio/tmp/vmatch_evaluation/spliced_3'
+   result_dir = '/fml/ag-raetsch/home/fabio/tmp/vmatch_evaluation/spliced_3/dataset'
 
-#map_1_fn = jp(working_dir,'map.vm.spliced')
-map_1_fn = jp(working_dir,'spliced.heuristic')
-map_2_fn = jp(working_dir,'map.vm')
+   map_1_fn = jp(main_dir,'map.vm.spliced')
+   map_2_fn = jp(spliced_dir,'map.vm')
 
-dg = DatasetGenerator(map_1_fn,map_2_fn)
-dg.compile_dataset()
-dg.saveAs(jp(result_dir,'dataset_neg_strand_testcase'))
+   dg = DatasetGenerator(map_1_fn,map_2_fn)
+   dg.compile_dataset()
+   dg.saveAs(jp(result_dir,'dataset_run_1.pickle'))
+
+if __name__ == '__main__':
+   #cProfile.run('run()')
+   run()