+ saving changes in the dataset generation
[qpalma.git] / tools / run_specific_scripts / transcriptome_analysis / createNewDataset.py
index 42ed713..e32dde5 100644 (file)
@@ -3,23 +3,25 @@
 
 import os.path
 
-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'
+#working_dir='/fml/ag-raetsch/share/projects/qpalma/solexa/new_run2/mapping/spliced'
 
-working_dir='/fml/ag-raetsch/share/projects/qpalma/solexa/new_run2/mapping/spliced'
+main_dir = '/fml/ag-raetsch/home/fabio/tmp/transcriptome_data/run_0/'
 
+#spliced_dir = '/media/oka_raid/backup/data/solexa_analysis/ATH/Transcriptome/Col-0/run_44/4/length_38/spliced'
+#result_dir = '/fml/ag-raetsch/home/fabio/tmp/transcriptome_data/run_1/'
 
-result_dir='/fml/ag-raetsch/home/fabio/tmp/sandbox'
+spliced_dir = '/media/oka_raid/backup/data/solexa_analysis/ATH/Transcriptome/Col-0/run_44/4/length_38/spliced_3'
+result_dir = '/fml/ag-raetsch/home/fabio/tmp/transcriptome_data/run_2/'
 
-#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.saveAs(jp(result_dir,'dataset_run_2.pickle'))