9017c225dfd0666af7dbc2dccd897506da6b3c50
[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 # The parameter you want to do prediction with:
43 #
44
45 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
46
47 #
48 # In order to align short reads QPalma relies on additional information such as
49 # splice site score prediction.
50 #
51
52 genome_dir = /fml/ag-raetsch/share/projects/genomes/A_thaliana_best/genome
53 acceptor_scores_loc = /fml/ag-raetsch/home/fabio/tmp/interval_query_files/acc
54 donor_scores_loc = /fml/ag-raetsch/home/fabio/tmp/interval_query_files/don
55
56 genome_file_fmt = chr%d.dna.flat
57 splice_score_file_fmt= contig_%d%s
58
59 #allowed_fragments = [1,2,3,4,5]
60 allowed_fragments = [1]
61
62
63 #
64 # Settings concerning the prediction algorithm
65 #
66
67 #
68 #
69 #
70
71
72
73 #
74 # This defines
75 #
76
77 half_window_size = 1500
78
79 #
80 # Settings concerning the training algorithm
81 #
82 #
83
84 optimizer = MOSEK
85 optimizer = CPLEX
86 optimizer = CVXOPT
87
88 #
89 # The output format can be one of BLAT, ShoRe or mGene
90 #
91
92 output_format = blat
93
94 #prb_offset = 50
95 prb_offset = 64
96
97 enable_quality_scores = True
98 enable_splice_scores = True
99 enable_intron_length = True
100
101 C = 100
102
103 remove_duplicate_scores = False
104
105 matchmatrixCols = 1
106 matchmatrixRows = 6
107 numAccSuppPoints = 10
108 numConstraintsPerRound = 50
109 numDonSuppPoints = 10
110 numLengthSuppPoints = 10
111 numQualPlifs = 30
112 numQualSuppPoints = 10
113
114 anzpath = 2
115
116 #enable_intron_length = True
117 #enable_quality_scores = True
118 #enable_splice_signals = True
119 #
120 iter_steps = 40
121 max_intron_len = 2000
122 max_qual = 40
123 max_svm_score = 1.0
124 min_intron_len = 20
125 min_qual = -5
126 min_svm_score = 0.0
127 print_matrix = False