+ fixed a parameter name bug in the exporter script

+ minor changes to qpalma

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7059 e1793c9e-67f9-0310-80fc-b846ff1f7b36

diff --git a/python/export_param.py b/python/export_param.py
index 5ddcd14..be830ce 100644 (file)
--- a/python/export_param.py
+++ b/python/export_param.py
@@ -8,11 +8,14 @@
 import bz2
 
 def writeStruct(fid,plif):
-   fid.write('%s_len_limits=%s\n'%(plif.name,str(plif.limits)))
-   fid.write('%s_len_penalties=%s\n'%(plif.name,str(plif.penalties)))
-   fid.write('%s_len_bins=%d\n'%(plif.name,len(plif.limits)))
+   fid.write('%s_limits=%s\n'%(plif.name,str(plif.limits)))
+   fid.write('%s_penalties=%s\n'%(plif.name,str(plif.penalties)))
+   fid.write('%s_bins=%d\n'%(plif.name,len(plif.limits)))
 
    if plif.name == 'intron':
+      fid.write('%s_len_limits=%s\n'%(plif.name,str(plif.limits)))
+      fid.write('%s_len_penalties=%s\n'%(plif.name,str(plif.penalties)))
+      fid.write('%s_len_bins=%d\n'%(plif.name,len(plif.limits)))
       fid.write('%s_len_min=%d\n'%(plif.name,plif.min_len))
       fid.write('%s_len_max=%d\n'%(plif.name,plif.max_len))
       fid.write('%s_len_transform=%s\n'%(plif.name,plif.transform))

diff --git a/python/paths_load_data_pickle.py b/python/paths_load_data_pickle.py
new file mode 100644 (file)
index 0000000..112ec5f
--- /dev/null
+++ b/python/paths_load_data_pickle.py
@@ -0,0 +1,50 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import cPickle
+
+def paths_load_data_pickle(expt,genome_info,PAR):
+   """
+      
+   """
+
+   # function [Sequences, Acceptors, Donors, Exons, Ests, Noises] = paths_load_data(expt,genome_info,PAR)
+   # Load the relevant file and return the alignment data
+
+   # expt can be 'training','validation' or 'test'
+
+   assert expt in ['training','validation','test']
+
+   tmp_dir = '/fml/ag-raetsch/home/fabio/tmp'
+
+   Noises = [];
+
+   if expt == 'training':
+      if PAR.microexon:
+         if PAR.LOCAL_ALIGN: # local version
+
+            train_data = '%s/microexon_train_data.pickle' % genome_info.basedir
+            data = cPickle.load(open(train_data))
+
+         else: # global version
+            pass
+
+
+      else:
+         train_data = '%s/exons_train_local.pickle' % genome_info.basedir
+         data = cPickle.load(open(train_data))
+
+      print 'train_data is %s' % train_data
+
+      Sequences = data['Train']       # dna sequences
+      Acceptors = data['TrainAcc']    # acceptor scores
+      Donors    = data['TrainDon']    # donor scores
+      Exons     = data['TrainExon']   # exon boundaries
+      Ests      = data['TrainEsts']   # est sequences
+     
+   # Lower all indices by one to convert matlab 
+   # to python indices
+
+   Exons -= 1
+
+   return Sequences, Acceptors, Donors, Exons, Ests, Noises

diff --git a/python/qpalma.py b/python/qpalma.py
index 271bde9..0b0b989 100644 (file)
--- a/python/qpalma.py
+++ b/python/qpalma.py
@@ -90,7 +90,8 @@ class QPalma:
       and N == len(Ests), 'The Seq,Accept,Donor,.. arrays are of different lengths'
       self.plog('Number of training examples: %d\n'% N)
 
-      iteration_steps = 200 ; #upper bound on iteration steps
+      #iteration_steps = 200 ; #upper bound on iteration steps
+      iteration_steps = 2 ; #upper bound on iteration steps
 
       remove_duplicate_scores = False
       print_matrix = False
@@ -127,7 +128,7 @@ class QPalma:
       #############################################################################################
       self.plog('Starting training...\n')
 
-      iteration_nr = 1
+      iteration_nr = 0
 
       while True:
          if iteration_nr == iteration_steps:
@@ -230,8 +231,6 @@ class QPalma:
             for i in range(num_path[exampleIdx]):
                AlignmentScores[i+1] = newAlignmentScores[i]
 
-            #print AlignmentScores
-               
             spliceAlign = spliceAlign.reshape(num_path[exampleIdx],dna_len)
             weightMatch = weightMatch.reshape(num_path[exampleIdx],mm_len)
             # Calculate weights of the respective alignments Note that we are
@@ -314,10 +313,10 @@ class QPalma:
                #
                # end of one example processing 
                #
-            if exampleIdx == 10:
-               break
+            #if exampleIdx == 100:
+            #   break
          
-         break
+         #break
 
          #
          # end of one iteration through all examples