python/paths_load_data.py

   1 #!/usr/bin/env python
   2 # -*- coding: utf-8 -*-
   3
   4 import io_pickle
   5 import scipy.io
   6 import pdb
   7
   8 def paths_load_data(expt,genome_info,PAR):
   9    """
  10
  11    """
  12
  13    # function [Sequences, Acceptors, Donors, Exons, Ests, Noises] = paths_load_data(expt,genome_info,PAR)
  14    # Load the relevant file and return the alignment data
  15
  16    # expt can be 'training','validation' or 'test'
  17
  18    assert expt in ['training','validation','test']
  19
  20    tmp_dir = '/fml/ag-raetsch/home/fabio/tmp'
  21
  22    Noises = [];
  23
  24    if expt == 'training':
  25       if PAR.microexon:
  26          if PAR.LOCAL_ALIGN: # local version
  27
  28             train_data = '%s/microexon_train_data_cut_local.mat' % genome_info.basedir
  29             train_data = '%s/microexon_train_data.mat' % genome_info.basedir
  30             #train_data_pickle = '%s/microexon_train_data_cut_local.pickle'% tmp_dir
  31             #io_pickle.convert_v6(train_data,train_data_pickle)
  32             #train_data = io_pickle.load(train_data_pickle)
  33             data = scipy.io.loadmat(train_data)
  34
  35          else: # global version
  36
  37             train_data = '%s/microexon_train_data_cut_ip=%1.3f_dp=%1.3f_mp=%1.3f.mat' %\
  38                (genome_info.basedir, PAR.insertion_prob, PAR.deletion_prob, PAR.mutation_prob)
  39
  40             train_data = '%s/microexon_train_data.mat' % genome_info.basedir
  41             #train_data_pickle = '%s/microexon_train_data_cut_ip=%1.3f_dp=%1.3f_mp=%1.3f.pickle' %\
  42             #   (tmp_dir, PAR.insertion_prob, PAR.deletion_prob, PAR.mutation_prob)
  43
  44             #io_pickle.convert_v6(train_data,train_data_pickle)
  45             #train_data = io_pickle.load(train_data_pickle)
  46             data = scipy.io.loadmat(train_data)
  47             Noises = data['TrainNoise'] # substitution matrix
  48
  49       else:
  50          train_data = '%s/exons_train_local.mat' % genome_info.basedir
  51          #train_data_pickle = '%s/exons_train_local.pickle'% tmp_dir
  52          #io_pickle.convert_v6(train_data,train_data_pickle)
  53          #microexon_train_data = io_pickle.load(train_data_pickle)
  54          data = scipy.io.loadmat(train_data)
  55
  56       print 'train_data is %s' % train_data
  57
  58       Sequences = data['Train']       # dna sequences
  59       Acceptors = data['TrainAcc']    # acceptor scores
  60       Donors    = data['TrainDon']    # donor scores
  61       Exons     = data['TrainExon']   # exon boundaries
  62       Ests      = data['TrainEsts']   # est sequences
  63
  64    #elif expt == 'validation':
  65    #  print('Loading validation data\n') ;
  66    #  if PAR.microexon,
  67    #    if PAR.LOCAL_ALIGN
  68    #      %local version
  69    #      load(sprintf('%s/microexon_val_data_cut_local_ip=%1.3f_dp=%1.3f_mp=%1.3f.mat', ...
  70    #         genome_info.basedir, PAR.insertion_prob, PAR.deletion_prob, PAR.mutation_prob),  ...
  71    #      'ValEsts', 'ValExon', 'Val', 'ValAcc', 'ValDon') ;
  72    #    else
  73    #      %global version
  74    #      load(sprintf('%s/microexon_val_data_cut_ip=%1.3f_dp=%1.3f_mp=%1.3f.mat', ...
  75    #         genome_info.basedir, PAR.insertion_prob, PAR.deletion_prob, PAR.mutation_prob),  ...
  76    #      'ValEsts', 'ValExon', 'Val', 'ValAcc', 'ValDon') ;
  77    #    end
  78    #  else
  79    #    load(sprintf('%s/exons_val_ip=%1.3f_dp=%1.3f_mp=%1.3f.mat', ...
  80    #       genome_info.basedir, PAR.insertion_prob, PAR.deletion_prob, PAR.mutation_prob),  ...
  81    #    'ValEsts', 'ValExon', 'Val', 'ValAcc', 'ValDon') ;
  82    #  end
  83    #
  84    #  Sequences = Val ;      % dna sequences
  85    #  Acceptors = ValAcc ;   % acceptor scores
  86    #  Donors    = ValDon ;   % donor scores
  87    #  Exons     = ValExon ;  % exon boundaries
  88    #  Ests      = ValEsts ;  % est sequences
  89
  90
  91
  92    #elif expt == 'test':
  93    #  fprintf('Loading test data\n') ;
  94    #  if PAR.microexon,
  95    #    if PAR.LOCAL_ALIGN
  96    #      %local version
  97    #      load(sprintf('%s/microexon_test_data_cut_local_ip=%1.3f_dp=%1.3f_mp=%1.3f.mat', ...
  98    #         genome_info.basedir, PAR.insertion_prob, PAR.deletion_prob, PAR.mutation_prob), ...
  99    #      'TestEsts', 'TestExon', 'Test', 'TestAcc', 'TestDon') ;
 100    #    else
 101    #      %global version
 102    #      load(sprintf('%s/microexon_test_data_cut_ip=%1.3f_dp=%1.3f_mp=%1.3f.mat', ...
 103    #         genome_info.basedir, PAR.insertion_prob, PAR.deletion_prob, PAR.mutation_prob),  ...
 104    #      'TestEsts', 'TestExon', 'Test','TestAcc', 'TestDon', 'TestNoise') ;
 105    #      Noises    = TestNoise ; % substitution matrix
 106    #      end
 107    #      else
 108    #    load(sprintf('%s/exons_test_ip=%1.3f_dp=%1.3f_mp=%1.3f.mat', ...
 109    #       genome_info.basedir, PAR.insertion_prob, PAR.deletion_prob, PAR.mutation_prob), ...
 110    #    'TestEsts', 'TestExon', 'Test', 'TestAcc', 'TestDon') ;
 111    #  end
 112    #
 113    #  Sequences = Test ;      % dna sequences
 114    #  Acceptors = TestAcc ;   % acceptor scores
 115    #  Donors    = TestDon ;   % donor scores
 116    #  Exons     = TestExon ;  % exon boundaries
 117    #  Ests      = TestEsts ;  % est sequences
 118
 119    return Sequences, Acceptors, Donors, Exons, Ests, Noises