+ changed output format of alignment file script to be compatible with est2gff
[qpalma.git] / scripts / grid_predict.py
index 54ed50a..2afeb7c 100644 (file)
@@ -45,7 +45,7 @@ def makeJobs(run,dataset_fn,chunks,param):
 
    for c_name,current_chunk in chunks:
       current_job = KybJob(grid_predict.g_predict,[run,dataset_fn,current_chunk,param,c_name])
 
    for c_name,current_chunk in chunks:
       current_job = KybJob(grid_predict.g_predict,[run,dataset_fn,current_chunk,param,c_name])
-      current_job.h_vmem = '5.0G'
+      current_job.h_vmem = '12.0G'
       #current_job.express = 'True'
 
       print "job #1: ", current_job.nativeSpecification
       #current_job.express = 'True'
 
       print "job #1: ", current_job.nativeSpecification
@@ -67,14 +67,14 @@ def create_and_submit():
    run   = cPickle.load(open(jp(run_dir,'run_obj.pickle')))
    param = cPickle.load(open(jp(run_dir,'param_526.pickle')))
 
    run   = cPickle.load(open(jp(run_dir,'run_obj.pickle')))
    param = cPickle.load(open(jp(run_dir,'param_526.pickle')))
 
-   dataset_fn           = '/fml/ag-raetsch/home/fabio/svn/projects/QPalma/scripts/dataset_12_05_08.test.pickle'
-   prediction_keys_fn   = '/fml/ag-raetsch/home/fabio/svn/projects/QPalma/scripts/dataset_12_05_08.test_keys.pickle'
+   dataset_fn           = '/fml/ag-raetsch/home/fabio/tmp/transcriptome_data/dataset_transcriptome_run_1.pickle'
+   prediction_keys_fn   = '/fml/ag-raetsch/home/fabio/tmp/transcriptome_data/dataset_transcriptome_run_1.keys.pickle'
 
    prediction_keys = cPickle.load(open(prediction_keys_fn))
 
    print 'Found %d keys for prediction.' % len(prediction_keys)
 
 
    prediction_keys = cPickle.load(open(prediction_keys_fn))
 
    print 'Found %d keys for prediction.' % len(prediction_keys)
 
-   num_splits = 15
+   num_splits = 25
    slices = get_slices(len(prediction_keys),num_splits)
    chunks = []
    for idx,slice in enumerate(slices):
    slices = get_slices(len(prediction_keys),num_splits)
    chunks = []
    for idx,slice in enumerate(slices):