4c8a65bbc66d56bde4de2249273902222cd18613
[qpalma.git] / test.conf
1 #
2 # Global settings
3 #
4
5
6 #
7 # Set this variable to True if you want to allow QPalma to perform more extensive checks
8 #
9
10 perform_checks = True
11
12 #
13 # You can set the platform.
14 # Currently supported:
15 #
16 # - Set IGA for Illumina Genome Analyzer
17 # - Set 454 for the Roche 454 platform (not implemented yet)
18
19 platform = IGA
20
21 #
22 # This variable stores the path to the toplevel result directory
23 #
24
25 result_dir = /fml/ag-raetsch/home/fabio/tmp/sandbox/first_test
26
27 #
28 # These variables store the filename of the raw read data
29 #
30
31 spliced_reads_fn = /fml/ag-raetsch/home/fabio/tmp/sandbox/map_2nd.vm
32
33 unspliced_reads_fn = /fml/ag-raetsch/home/fabio/tmp/sandbox/map.vm
34
35 #
36 # You can specify how many nodes you want to use via this variable
37 #
38
39 num_splits = 5
40
41 #
42 # Specifiy here the filename of the global logfile QPalma uses to report everything
43 #
44
45 global_log_fn = /fml/ag-raetsch/home/fabio/tmp/sandbox/first_test/qpalma.log
46
47 #
48 # The parameter you want to do prediction with:
49 #
50
51 prediction_param_fn = /fml/ag-raetsch/home/fabio/tmp/newest_run/alignment/run_enable_quality_scores_+_enable_splice_signals_+_enable_intron_length_+/param_526.pickle
52
53 #
54 # In order to align short reads QPalma relies on additional information such as
55 # splice site score prediction.
56 #
57
58 genome_dir = /fml/ag-raetsch/share/projects/genomes/A_thaliana_best/genome
59 acceptor_scores_loc = /fml/ag-raetsch/home/fabio/tmp/interval_query_files/acc
60 donor_scores_loc = /fml/ag-raetsch/home/fabio/tmp/interval_query_files/don
61
62 genome_file_fmt = chr%d.dna.flat
63 splice_score_file_fmt= contig_%d%s
64
65 #allowed_fragments = [1,2,3,4,5]
66 allowed_fragments = [1]
67
68
69 #
70 # Settings concerning the prediction algorithm
71 #
72
73 #
74 #
75 #
76
77
78
79 #
80 # This defines
81 #
82
83 half_window_size = 1500
84
85 #
86 # Settings concerning the training algorithm
87 #
88 #
89
90 optimizer = MOSEK
91 optimizer = CPLEX
92 optimizer = CVXOPT
93
94 #
95 # The output format can be one of BLAT, ShoRe or mGene
96 #
97
98 output_format = BLAT
99
100 #prb_offset = 50
101 prb_offset = 64
102
103 enable_quality_scores = True
104 enable_splice_scores = True
105 enable_intron_length = True
106
107 C = 100
108
109 remove_duplicate_scores = False
110
111 matchmatrixCols = 1
112 matchmatrixRows = 6
113 numAccSuppPoints = 10
114 numConstraintsPerRound = 50
115 numDonSuppPoints = 10
116 numLengthSuppPoints = 10
117 numQualPlifs = 30
118 numQualSuppPoints = 10
119
120 anzpath = 2
121
122 #enable_intron_length = True
123 #enable_quality_scores = True
124 #enable_splice_signals = True
125 #
126 iter_steps = 40
127 max_intron_len = 2000
128 max_qual = 40
129 max_svm_score = 1.0
130 min_intron_len = 20
131 min_qual = -5
132 min_svm_score = 0.0
133 print_matrix = False
134 totalQualSuppPoints = 300