+ changed check for intial setting of old_w. (matrix != None does not work in cvxopt)
[qpalma.git] / test.conf
index 3ca1d96..9eb7f82 100644 (file)
--- a/test.conf
+++ b/test.conf
@@ -28,9 +28,9 @@ result_dir = /fml/ag-raetsch/home/fabio/tmp/sandbox/first_test
 # These variables store the filename of the raw read data
 #
 
-spliced_reads_fn = /fml/ag-raetsch/home/fabio/tmp/sandbox/map_2nd.vm
+#spliced_reads_fn = /fml/ag-raetsch/home/fabio/tmp/sandbox/map_2nd.vm
 
-unspliced_reads_fn = /fml/ag-raetsch/home/fabio/tmp/sandbox/map.vm
+#unspliced_reads_fn = /fml/ag-raetsch/home/fabio/tmp/sandbox/map.vm
 
 #
 # You can specify how many nodes you want to use via this variable
@@ -38,24 +38,6 @@ unspliced_reads_fn = /fml/ag-raetsch/home/fabio/tmp/sandbox/map.vm
 
 num_splits = 5
 
-#
-# Specifiy here the filename of the global logfile QPalma uses to report everything
-#
-
-global_log_fn = /fml/ag-raetsch/home/fabio/tmp/sandbox/first_test/qpalma.log
-
-#
-# The parameter you want to do prediction with:
-#
-
-prediction_parameter_fn = /fml/ag-raetsch/home/fabio/tmp/newest_run/alignment/run_enable_quality_scores_+_enable_splice_signals_+_enable_intron_length_+/param_526.pickle
-
-#
-# The run object which should become at some point obsolete but is still needed for now
-#
-
-run_fn = /fml/ag-raetsch/home/fabio/tmp/newest_run/alignment/run_enable_quality_scores_+_enable_splice_signals_+_enable_intron_length_+/run_obj.pickle
-
 #
 # In order to align short reads QPalma relies on additional information such as
 # splice site score prediction.
@@ -93,24 +75,47 @@ half_window_size = 1500
 #
 #
    
-numLengthSuppPoints  = 10
-numDonSuppPoints     = 10
-numAccSuppPoints     = 10
-matchmatrixRows      = 10
-matchmatrixCols      = 10
-numQualSuppPoints    = 10
-totalQualSuppPoints  = 10
-
 optimizer = MOSEK
 optimizer = CPLEX
 optimizer = CVXOPT
 
 #
-# BLAT, ShoRe and mGene
+# The output format can be one of BLAT, ShoRe or mGene
 #
 
-output_format = BLAT
-
+output_format = blat
 
 #prb_offset = 50
 prb_offset = 64
+
+enable_quality_scores = True
+enable_splice_scores = True
+enable_intron_length = True
+
+C = 100
+
+remove_duplicate_scores = False
+
+matchmatrixCols         = 1
+matchmatrixRows         = 6
+numAccSuppPoints        = 10
+numConstraintsPerRound  = 50
+numDonSuppPoints        = 10
+numLengthSuppPoints     = 10
+numQualPlifs            = 30
+numQualSuppPoints       = 10
+
+anzpath                 = 2
+
+#enable_intron_length    = True
+#enable_quality_scores   = True
+#enable_splice_signals   = True
+#
+iter_steps              = 40
+max_intron_len          = 2000
+max_qual                = 40
+max_svm_score           = 1.0
+min_intron_len          = 20
+min_qual                = -5
+min_svm_score           = 0.0
+print_matrix            = False