qpalma/Configuration.py

   1 #!/usr/bin/env python
   2 # -*- coding: utf-8 -*-
   3
   4 import numpy.matlib
   5 import os.path
   6 import cPickle
   7
   8 ###############################################################################
   9 #
  10 # Load a random but fixed initial parameter vector this makes debugging easier
  11 #
  12 ###############################################################################
  13
  14 fixedParamQ = cPickle.load(open('/fml/ag-raetsch/home/fabio/svn/projects/QPalma/scripts/randInitParam.pickle'))
  15
  16 ###########################################################
  17 #
  18 # The parameters for the QPalma algorithm
  19 #
  20 #
  21 C = 1
  22
  23 min_intron_len = 20
  24 max_intron_len = 2000
  25
  26 min_svm_score = 0.0
  27 max_svm_score = 1.0
  28
  29 ###############################################################################
  30 #
  31 # CHOOSING THE MODE
  32 #
  33 # 'normal' means work like Palma 'using_quality_scores' means work like Palma
  34 # plus using sequencing quality scores
  35 #
  36 ###############################################################################
  37
  38 #mode = 'normal'
  39 mode = 'using_quality_scores'
  40
  41 ###############################################################################
  42 #
  43 # When using quality scores our scoring function is defined as
  44 #
  45 # f: S_e x R x S -> R
  46 #
  47 # where S_e is {A,C,G,T,N} and S = {A,C,G,T,N,-}
  48 #
  49 # as opposed to a usage without quality scores when we only have
  50 #
  51 # f: S x S -> R
  52 #
  53 # The matrix of plifs is defined as follows:
  54 #
  55 #  elem |   -  a  c  g  t  n
  56 #  -------------------------
  57 #  idx  |   0  1  2  3  4  5
  58 #
  59 #
  60 #              dna
  61 #
  62 #           -  a  c  g  t  n
  63 #        a
  64 # est    c
  65 #        g
  66 #        t
  67 #        n
  68 #
  69 # so the index can be calculated as (estnum-1)*6 + dnanum.
  70 #
  71 # At ests we do not have gaps with quality scores so we look up the matchmatrix
  72 # instead.
  73 ###############################################################################
  74
  75 #numLengthSuppPoints  = 30
  76 #numDonSuppPoints     = 30
  77 #numAccSuppPoints     = 30
  78 #numQualSuppPoints    = 16
  79
  80 numLengthSuppPoints  = 20
  81 numDonSuppPoints     = 20
  82 numAccSuppPoints     = 20
  83 numQualSuppPoints    = 4
  84
  85 min_qual = -1
  86 max_qual = 40
  87
  88 USE_OPT = True
  89
  90 if mode == 'normal':
  91    sizeMatchmatrix   = (6,6)
  92    estPlifs = 0
  93    dnaPlifs = 0
  94    numQualPlifs = estPlifs*dnaPlifs
  95 elif mode == 'using_quality_scores':
  96    sizeMatchmatrix   = (6,1)
  97    estPlifs = 5
  98    dnaPlifs = 6
  99    numQualPlifs = estPlifs*dnaPlifs
 100 else:
 101    assert False, 'Wrong operation mode specified'
 102
 103 totalQualSuppPoints = numQualPlifs*numQualSuppPoints
 104
 105 numFeatures = numDonSuppPoints + numAccSuppPoints\
 106 + numLengthSuppPoints + sizeMatchmatrix[0]*sizeMatchmatrix[1] + totalQualSuppPoints
 107
 108
 109 ###############################################################################
 110 #
 111 # GENERAL SETTINGS CONCERNING THE SOLVER
 112 #
 113 #
 114 #
 115 ###############################################################################
 116
 117 iter_steps = 40
 118 remove_duplicate_scores = False
 119 print_matrix            = False
 120 anzpath                 = 2
 121
 122 if mode == 'normal':
 123    fixedParam = fixedParam[:numFeatures]
 124 elif mode == 'using_quality_scores':
 125    fixedParam = fixedParamQ[:numFeatures]
 126 else:
 127    assert False, 'Wrong operation mode specified'
 128
 129 ###############################################################################
 130 #
 131 # DATA SETTINGS CONCERNING THE SPLITS AND FILE LOCATIONS
 132 #
 133 #
 134 #
 135 ###############################################################################
 136
 137 training_begin    =    0
 138 training_end      = 2000
 139
 140 prediction_begin  = 2000
 141 prediction_end    = 3500
 142
 143 joinp = os.path.join
 144
 145 tmp_dir              = '/fml/ag-raetsch/home/fabio/tmp/solexa_tmp'
 146 data_path            = '/fml/ag-raetsch/share/projects/qpalma/solexa'
 147
 148 original_path  = joinp(data_path,'original_solexa_data')
 149 annot_path     = joinp(data_path,'annotation_data')
 150 remapped_path  = joinp(data_path,'remapped_solexa_data')
 151
 152 dna_flat_fn    =  '/fml/ag-raetsch/share/projects/genomes/A_thaliana_best/genome/'
 153 gff_fn         = joinp(annot_path,'TAIR7_GFF3_genes_Chr%s.gff_v1')
 154 filtered_fn    = joinp(data_path,'allFilteredReads_04_02_2008')
 155 remapped_fn    = joinp(remapped_path,'map_best_hit.18.unambig')
 156
 157 dataset_fn = '/fml/ag-raetsch/home/fabio/svn/projects/QPalma/scripts/chr1_dataset.pickle'
 158
 159 ###############################################################################
 160 #
 161 # SANITY CHECKS
 162 #
 163 ###############################################################################
 164 assert numQualPlifs       >= 0
 165 assert numDonSuppPoints    > 1
 166 assert numAccSuppPoints    > 1
 167 assert numLengthSuppPoints > 1
 168 assert numQualSuppPoints   > 1
 169
 170 assert os.path.exists(dna_flat_fn), 'DNA data does not exist!'
 171 assert os.path.exists(filtered_fn), 'EST/Reads data does not exist!'
 172 assert os.path.exists(remapped_fn), 'EST/Reads data does not exist!'