+ check in latest changes
authorfabio <fabio@e1793c9e-67f9-0310-80fc-b846ff1f7b36>
Wed, 23 Jan 2008 09:16:43 +0000 (09:16 +0000)
committerfabio <fabio@e1793c9e-67f9-0310-80fc-b846ff1f7b36>
Wed, 23 Jan 2008 09:16:43 +0000 (09:16 +0000)
TODO
+ rearrange directory structure a bit

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7534 e1793c9e-67f9-0310-80fc-b846ff1f7b36

python/Configuration.py
python/paths_load_data_solexa.py
python/qpalma.py
python/qpalma_predict.py

index 5eb7d4c..7d82c0c 100644 (file)
@@ -108,7 +108,7 @@ fixedParam = numpy.matlib.mat([[ 0.62870709], [ 0.7012026 ], [ 0.60236784],
 #
 #
 
 #
 #
 
-C = 1000.0
+C = 100000.0
 
 # 'normal' means work like Palma 'using_quality_scores' means work like Palma
 # plus using sequencing quality scores
 
 # 'normal' means work like Palma 'using_quality_scores' means work like Palma
 # plus using sequencing quality scores
index cb9565d..8d0dc5c 100644 (file)
@@ -6,10 +6,6 @@ import cPickle
 import pdb
 
 def paths_load_data_solexa(expt,genome_info,PAR):
 import pdb
 
 def paths_load_data_solexa(expt,genome_info,PAR):
-   """
-      
-   """
-
    # expt can be 'training','validation' or 'test'
    assert expt in ['training','validation','test']
 
    # expt can be 'training','validation' or 'test'
    assert expt in ['training','validation','test']
 
@@ -39,9 +35,7 @@ def paths_load_data_solexa(expt,genome_info,PAR):
       assert len(prb) == len(seq)
 
       currentGene = allGenes[gene_id]
       assert len(prb) == len(seq)
 
       currentGene = allGenes[gene_id]
-
-      #seq = seq.lower().replace('n','a')
-      seq = seq.lower()#.replace('n','a')
+      seq = seq.lower()
 
       try:
          currentSeq = tair7_seq[gene_id+'.1']['sequence'].lower()
 
       try:
          currentSeq = tair7_seq[gene_id+'.1']['sequence'].lower()
index ea5e924..412a67b 100644 (file)
@@ -72,9 +72,9 @@ class QPalma:
          Sequences, Acceptors, Donors, Exons, Ests, Qualities = loadArtificialData(1000)
          use_quality_scores = False
       elif Configuration.mode == 'using_quality_scores':
          Sequences, Acceptors, Donors, Exons, Ests, Qualities = loadArtificialData(1000)
          use_quality_scores = False
       elif Configuration.mode == 'using_quality_scores':
-         #Sequences, Acceptors, Donors, Exons, Ests, Qualities = paths_load_data_solexa('training',self.genome_info,self.ARGS)
+         Sequences, Acceptors, Donors, Exons, Ests, Qualities = paths_load_data_solexa('training',self.genome_info,self.ARGS)
 
 
-         Sequences, Acceptors, Donors, Exons, Ests, Qualities = loadArtificialData(1000)
+         #Sequences, Acceptors, Donors, Exons, Ests, Qualities = loadArtificialData(1000)
 
          #Sequences_, Acceptors_, Donors_, Exons_, Ests_, Qualities_ = generateData(100)
 
 
          #Sequences_, Acceptors_, Donors_, Exons_, Ests_, Qualities_ = generateData(100)
 
index c39d9c3..db3c1cc 100644 (file)
@@ -73,8 +73,8 @@ class QPalma:
          use_quality_scores = False
 
       elif Conf.mode == 'using_quality_scores':
          use_quality_scores = False
 
       elif Conf.mode == 'using_quality_scores':
-         #Sequences, Acceptors, Donors, Exons, Ests, Qualities = paths_load_data_solexa('training',self.genome_info,self.ARGS)
-         Sequences, Acceptors, Donors, Exons, Ests, Qualities = loadArtificialData(1000)
+         Sequences, Acceptors, Donors, Exons, Ests, Qualities = paths_load_data_solexa('training',self.genome_info,self.ARGS)
+         #Sequences, Acceptors, Donors, Exons, Ests, Qualities = loadArtificialData(1000)
 
          #Sequences, Acceptors, Donors, Exons, Ests, Noises = paths_load_data_pickle('training',self.genome_info,self.ARGS)
          pdb.set_trace()
 
          #Sequences, Acceptors, Donors, Exons, Ests, Noises = paths_load_data_pickle('training',self.genome_info,self.ARGS)
          pdb.set_trace()
@@ -99,7 +99,7 @@ class QPalma:
 
       # Initialize parameter vector  / param = numpy.matlib.rand(126,1)
       #param_filename = '/fml/ag-raetsch/home/fabio/svn/projects/QPalma/python/elegans.param'
 
       # Initialize parameter vector  / param = numpy.matlib.rand(126,1)
       #param_filename = '/fml/ag-raetsch/home/fabio/svn/projects/QPalma/python/elegans.param'
-      param_filename='/fml/ag-raetsch/home/fabio/svn/projects/QPalma/python/param_30.pickle'
+      param_filename='/fml/ag-raetsch/home/fabio/svn/projects/QPalma/python/param_16.pickle'
       param = load_param(param_filename)
 
       # Set the parameters such as limits penalties for the Plifs
       param = load_param(param_filename)
 
       # Set the parameters such as limits penalties for the Plifs